Optical reader for analyte testing

ABSTRACT

Analyte collection and testing systems and methods, and more particularly to disposable oral fluid collection and testing systems and methods. Described herein are methods and apparatuses to achieve significant improvements in the detection of fluorescence signals in the reader.

CROSS REFERENCE TO RELATED APPLICATIONS

This patent application is a continuation of U.S. patent applicationSer. No. 16/223,096, filed Dec. 17, 2018, titled “OPTICAL READER FORANALYE TESTING,” now U.S. Pat. No. 11,262,367, which claims priority toU.S. Provisional Patent Application No. 62/599,671, filed on Dec. 15,2017, titled “POLARIZATION MAINTAINING OPTICAL PATH FOR ENSURING READERTO READER CONSISTENCY” and U.S. Provisional Patent Application No.62/599,674, filed on Dec. 15, 2017, titled “CLAMP DESIGN FOR PRECISIONALIGNMENT OF THE CARTRIDGE,” each of which is herein incorporated byreference in its entirety

This patent application may also be related to U.S. patent applicationSer. No. 16/040,506, filed on Jul. 19, 2018, now U.S. Pat. No.10,660,619, titled “CARTRIDGES FOR ORAL FLUID ANALYSIS AND METHODS OFUSE,” which claims priority to U.S. Provisional Patent Application No.62,534,394, titled “ORAL FLUID ANALYZING SYSTEMS AND METHODS” and filedJul. 19, 2017.

INCORPORATION BY REFERENCE

All publications and patent applications mentioned in this specificationare herein incorporated by reference in their entirety to the sameextent as if each individual publication or patent application wasspecifically and individually indicated to be incorporated by reference.

FIELD

Embodiments of the invention relate generally to analyte collection andtesting systems and methods, and more particularly to disposable oralfluid collection and testing systems and methods. Described herein aremethods and apparatuses to achieve significant improvements in thedetection of fluorescence signals in the reader.

BACKGROUND

Detection of analytes, particularly for drugs of abuse, is important invarious workplace drug testing settings, such as for pilots,professional athletes, and law enforcement, and to detect driving underthe influence of drugs (DUID). Detection of these analytes in oralfluid, i.e. saliva, provides a more convenient method of samplecollection than collection of blood or urine.

Conventionally, the collected samples are sent to a certified testinglaboratory for analysis. However, sending the samples to the lab andthen waiting for the lab to process and testing the sample and thenreport the results can take a significant amount of time, typically atleast days. In many situations, it would be desirable to have testingresults at the point of testing instead of waiting days for results fromthe lab. This would allow, for example, an airline to prevent pilotsunder the influence of drugs to fly a plane, thereby improving safety.

Tools for reading a sample-containing cartridge (e.g., a “reader”) mayutilize a detection scheme utilizing an optical sensor for reading thecartridge.

SUMMARY OF THE DISCLOSURE

Described herein are methods and apparatuses for how to achieve robustoptical performance of a sample cartridge reader with the use ofpolarization maintaining components in the optical path. The inherentnature of the optical coupling to almost any photonic chip is highlypolarization dependent in addition to the propagation through waveguidesand also evanescent coupling of light to molecules, including biologicalmolecules. Thus by fixing the polarization state of all four excitationchannels to the optical transverse-magnetic (TM) polarization asdescribed herein, we may achieve optimal and reliable performance of oursystem.

This embodiment of the invention utilizes polarization-maintainingoptical components in the optical path of the reader hardware. Theexcitation laser may be pigtailed with a polarization maintaining fiberand the scan head fiber is also polarization maintaining. Withelectromagnetic (EM) simulations of the photonic chip, we obtain theoptimal polarization state (TM) to use with this photonic chiparchitecture. This leads to a stable and repeatable known polarizationstate of light exiting the scan head and coupling into the photonicchip.

Also described herein are methods and apparatuses for use with analyteholding cartridges.

For example, described herein are optical reader devices for reading aphotonic chip of a removable cartridge. An optical reader device mayinclude: a cartridge holder comprising a slot extending into the reader,the slot having a height and a width; a scan head, wherein the scan headcomprises a first plurality of optical fiber ends that are opticallyconnected to one or more laser light sources and a second plurality offiber ends that are optically connected to a plurality of detectors; ascan head actuator configured to move the scan head relative to thecartridge holder; a plurality of valves on the cartridge holder that areconfigured to couple with valve openings in the removable cartridge; apump membrane actuator on the cartridge holder that is configured toapply force to a membrane pump of the removable cartridge, wherein thepump membrane actuator is configured to hold a plurality of extendedpositions to deflect or relax deflection of the membrane pump; and acontroller configured to coordinate movement of the scan head,illumination of the one or more laser light sources, detection by theplurality of detectors, opening and closing of the plurality of valvesand positioning of the pump membrane actuator when the removablecartridge is inserted into the cartridge holder.

An optical reader device for reading a photonic chip of a removablecartridge may include: a reader housing including a cartridge interfacecomprising an opening into the reader housing; a cartridge holdercomprising a slot extending into the reader from the cartridgeinterface, the slot having a height and a width; a scan head within thereader housing, wherein the scan head comprises a first plurality ofoptical fiber ends that are optically connected to one or more laserlight sources and a second plurality of fiber ends that are opticallyconnected to a plurality of detectors, further wherein the optical fiberends within the first and second plurality of optical fiber ends arearranged in a line; a scan head actuator configured to move the scanhead relative to the cartridge holder; a plurality of valves on thecartridge holder that are configured to couple with valve openings inthe removable cartridge; a pump membrane actuator comprising a rockerarm having a rounded end, wherein the pump membrane actuator isconfigured to apply force to a membrane pump of the removable cartridge,wherein the pump membrane actuator is configured to hold a plurality ofextended positions to deflect or relax deflection of the membrane pump;and a controller configured to coordinate movement of the scan head,illumination of the one or more laser light sources, detection by theplurality of detectors, opening and closing of the plurality of valvesand positioning of the pump membrane actuator when the removablecartridge is inserted into the cartridge interface.

In any of these variations, the device may also include one or more(e.g., a plurality of) fluid sensors in communication with thecontroller and configured to optically detect fluid within one or moreregions of the removable cartridge. The controller may be configured toclamp the cartridge holder when the removable cartridge is inserted into the cartridge holder. For example, the cartridge holder may include amovable/lockable base that may be driven to clamp the cartridge inposition.

The scan head may include a linear array of the first plurality ofoptical fiber ends and the second plurality of optical fiber ends. Afiber mount holder may hold the ends of the fibers (and in somevariations a lens or lensing material, filter, etc.) to the scan head.

Each valve of the plurality of valves may comprise a seal configured tobe moved relative to the cartridge holder to open or close a valveopening in the removable cartridge when the removable cartridge is heldwithin the cartridge holder. The seal may block or unblock an opening(valve opening) on a cartridge.

The pump membrane actuator may be any appropriate actuator (e.g.,mechanical, electromechanical, pneumatic, etc.), for example, the pumpmembrane actuator may comprise an arm and a driver. The pump membraneactuator may comprise a rounded, ball-shaped end. In some variations thepump membrane actuator comprises a rocker arm that is motor driven.

Any of these device may include a second actuator, such as a blisterpack arm on the cartridge holder, that is configured to apply force to ablister pack of the removable cartridge (e.g., to open/break the blisterpack).

Any of these devices may include a temperature sensor on the cartridgeholder and a heater on the cartridge holder, wherein the controller isfurther configured to regulate a temperature of a removable cartridgeheld in the cartridge holder.

In any of these variations, the reader may be configured for precisecontrol of the alignment of the cartridge relative to the scan head. Forexample, described herein are optical reader devices for reading aphotonic chip of a removable cartridge that include: a cartridge holdercomprising a slot extending in a z-axis into the reader, the slot havinga height in the y-axis direction and a width in the x-axis direction, aball plunger on one side of the slot, the ball plunger biased to extendinto the slot in the x-axis direction, configured to drive the removablecartridge against a reference surface in the z-axis and a referencesurface in the x-axis; a movable clamp base configured to apply force inthe y-axis to secure the removable cartridge within the slot and todrive the removable cartridge against a reference surface in the y-axis;a scan head configured to move relative to the cartridge holder, whereinthe scan head comprises a first plurality of fiber ends opticallyconnected to one or more laser light sources and a second plurality offiber ends optically connected to a plurality of detectors; and acontroller configured to coordinate movement of the movable clamp,movement of the scan head, illumination of the one or more laser lightsources and detection by the plurality of detectors.

For example, an optical reader device for reading a photonic chip of aremovable cartridge may include: a reader housing including a cartridgeinterface comprising an opening into the reader housing; a cartridgeholder comprising a slot extending in a z-axis into the reader, the slothaving a height in the y-axis direction and a width in the x-axisdirection, a ball plunger on one side of the slot, the ball plungerbiased to extend into the slot in the x-axis direction, configured todrive the removable cartridge against a reference surface in the z-axisand a reference surface in the x-axis; a movable clamp base configuredto apply force in the y-axis to secure the removable cartridge withinthe slot and to drive the removable cartridge against a referencesurface in the y-axis; a scan head configured to move relative to thecartridge holder, wherein the scan head comprises a first plurality offiber ends optically connected to one or more laser light sources and asecond plurality of fiber ends optically connected to a plurality ofdetectors; a pump membrane actuator configured to apply force to amembrane pump of the removable cartridge, wherein the pump membraneactuator is configured to hold a plurality of extended positions todeflect or relax deflection of the membrane pump; and a controllerconfigured to coordinate movement of the movable clamp, movement of thescan head, illumination of the one or more laser light sources anddetection by the plurality of detectors.

In some variations the reference surface in the z-axis is a pinextending into the cartridge slot.

Any of these devices may further include a scan head actuator configuredto move the scan head relative to the cartridge holder. The scan headactuator may be a motor.

As mentioned above, any of these devices may include one or a pluralityof valves on the cartridge holder that are configured to couple withvalve openings in the removable cartridge. The devices may include apump membrane actuator on the cartridge holder that is configured toapply force to a membrane pump of the removable cartridge, wherein thepump membrane actuator is configured to hold a plurality of extendedpositions to deflect or relax deflection of the membrane pump. Forexample, the pump membrane actuator may comprise an arm and a driver.Any of the pump membrane actuators may have an end that contacts thepump membrane that is configured to uniformly apply force (or todistribute the force) to the pump membrane to prevent damaging it. Insome variations the pump membrane actuator comprises a rounded,ball-shaped end. In some variations the pump membrane actuator comprisesa rocker arm that is motor driven.

As mentioned, any of these devices may include a plurality of fluidsensors in communication with the controller and configured to opticallydetect fluid within one or more regions of the removable cartridge. Thecontroller may be configured to clamp the movable clamp base to applyforce in the y-axis to secure the removable cartridge when the removablecartridge is inserted in to the cartridge holder.

The scan head may comprise a linear array of the first plurality ofoptical fiber ends and the second plurality of optical fiber ends, asdescribed above.

Any of these devices may include a second actuator (similar to the pumpmembrane actuator) that is configured to rupture one or more blisterpacks on the cartridge. For example, any of these apparatuses mayinclude a blister pack arm on the cartridge holder configured to applyforce to a blister pack of the removable cartridge.

The devices described herein may include one or more temperature sensorson the cartridge holder and/or a heater on the cartridge holder, whereinthe controller is further configured to regulate a temperature of aremovable cartridge held in the cartridge holder.

Any of the optical reader devices described herein may be part of asystem that may further include one or more cartridges as describedherein. Any of the reader variations described herein may be used withany of these cartridges to form a system; one or more additionalcomponents (outputs, displays, user interface software, etc.) may alsobe included.

Also described herein are devices (e.g., optical reader devices) forreading a photonic chip of a removable cartridge that are configured tocontrol the polarization of the energy applied so that it matches theinherent polarization of the photonic chip. For example described hereinare optical reader devices comprising: a scan head; a plurality of lasersources each configured to emit light having a TM polarization; a firstplurality of optical fibers, wherein each laser source is coupled to oneoptical fiber of the first plurality of optical fibers, further whereinthe first plurality of optical fibers are polarization maintainingsingle-mode fibers; a plurality of optical sensors; a second pluralityof optical fibers, wherein each optical sensor is coupled to one opticalfiber of the second plurality of optical fibers, further wherein thesecond plurality of optical fibers are multimode fibers; wherein each ofthe first plurality of optical fibers and the second plurality ofoptical fibers terminates on the scan head so that an end of eachoptical fiber of the first and second pluralities of optical fibers arearranged in a line facing a gap; and a cartridge holder configured toreceive the removable cartridge so that the photonic chip is alignedwith a polarization axis formed by the scan head so that an end of thephotonic chip comprising a plurality of waveguides faces the gap, acrossfrom the scan head, wherein the device is configured to maintain thepolarization of the polarization axis in a transverse-magnetic (TM)polarization.

The laser sources may comprise one or more diode lasers. The secondplurality of fibers may contain at least twice as many optical fibers asthe first plurality of fibers (e.g., there may be two optical fibers inthe first plurality and four optical fibers in the second plurality,there may be four optical fibers in the first plurality and nine opticalfibers in the second plurality, etc.).

The controller may be configured to control alignment of the scan headrelative to the cartridge. For example, the cartridge holder may beconfigured to clamp the cartridge to prevent it from moving. In somevariations, the cartridge holder may be configured to bias the cartridgein a direction that is normal to a major plane of the cartridge (e.g.,in a y-axis direction) against a reference surface to prevent movementof the cartridge as one or more actuators apply force to the cartridgeto drive fluid through the cartridge. This may reduce or eliminatemisalignment of the chip relative to the scan head during operation. Inany of these variations, the controller may be configured to adjust theposition of the scan head during operation of the device by actuating ascan head actuator to align the ends of the optical fibers withwaveguides of the photonic chip when the cartridge is in the cartridgeholder.

Also described herein are methods of operation of any of the devices andsystems described. For example, a method of reading optical signals froma photonic chip of a removable cartridge head in an optical reader mayinclude: aligning a scan head of the optical reader with the chip sothat the chip and a laser source, a plurality of fibers, and an opticalsensor of the scan head are aligned along a polarization axis with thechip; maintaining a polarization of the polarization axis in atransverse-magnetic (TM) polarization; emitting one or more beams oflight from the laser, through the plurality of fibers and into an edgeof the photonic chip in the TM polarization; and detecting, in theoptical sensor, TM polarized light from one or more waveguides withinthe chip when the one or more beams of light interact with an analytemolecule on the chip.

Any of these methods may include inserting a cartridge containing thechip into the optical reader.

Emitting may comprise emitting a plurality of concurrent beams of TMpolarized light from the scan head, into the edge of the photonic chip.

Maintaining the polarization of the polarization axis comprisesmaintaining the polarization of the plurality of fibers (e.g., the firstand/or second plurality of fibers).

The method may also comprise polarizing light emitted from the scan tothe edge of the chip in a polarizer.

The methods described herein may also include adjusting the alignment ofthe scan head while emitting and/or detecting to maintain the TMpolarization.

Any of the methods described herein may include inserting the cartridgeinto the reader device. Any of these methods may include clamping thecartridge and/or aligning the cartridge within the cartridge holder(e.g., clamp). For example, the cartridge may be inserted so that a ballplunger rides against a wall of the cartridge until it reaches a seatingedge of the cartridge, when a back surface (e.g., a z-face) of thecartridge contacts a reference surface. The ball plunger may drive thecartridge against two or more seating surfaces, including a seatingsurface in the x-axis and the back (z-face) seating surface(s). Onceseated, the controller may then lock the cartridge into position byclamping a y-face seating surface (e.g., a bottom of the cartridgeholder) against the cartridge. The controller may control alignment ofthe scan head with the photonics chip, as described herein. Thecontroller may coordinate fluid control of the cartridge and testing(applying light and detecting signals). For example, the controller maycoordinate one or more of: puncturing one or more blister pack, movingthe control solutions, moving the sample, dissolving reagents (e.g.,labeled antibodies for one or more targets, e.g., drugs of addition)into a control solution, dissolving reagents into the sample, mixing thecontrol solution, mixing the sample, moving the control solution intoone or more test wells in the photonics chip, emitting light through allor some of the first plurality of fibers, detecting evanescent signalsfrom the photonics chips from one or more of the second plurality offibers, moving the sample into the one or more test wells of thephotonics chip, and detecting evanescent signals from the photonicschips from one or more of the second plurality of fibers. In somevariations the method may include testing the control solution in thesame well as the sample solution. The controller may coordinate any orall of these steps and may repeat any of these steps.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe claims that follow. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings, of which:

FIG. 1 is a top view of an embodiment of a disposable device thatincludes an integrated oral fluid collection device and cartridge forprocessing and testing the collected sample.

FIG. 2 is an exploded view of the components of the disposable deviceshown in FIG. 1.

FIGS. 3A and 3B illustrate a top perspective view and bottom perspectiveview, respectively, of a bottom part of the cartridge attached to thesaliva collection device.

FIG. 4A illustrates a top view of the bottom part of the cartridgeattached to the saliva collection device.

FIG. 4B illustrates a perspective view of the bottom part of thecartridge attached to a cross-sectional view of the saliva collectiondevice.

FIG. 4C illustrates a close up view of a piercing element using topuncture a blister pack.

FIGS. 4D and 4E show front perspective and back perspectives,respectively of an example of a distal end of a saliva collectionsystem, showing the collection body and two swab pistons extendingdistally from the collection.

FIGS. 5A and 5B illustrate a top perspective view and a bottomperspective view, respectively, of a top part of the cartridge.

FIGS. 5C and 5D show a top and bottom, respectively, or an example of acartridge body.

FIGS. 6A and 6B illustrate a perspective view and a cross-sectionalview, respectively, of a cap for the saliva collection device.

FIG. 6C shows a section through a top of an example of a salivacollection system (with the front side removed).

FIG. 6D shows a perspective view of the exemplary saliva collectionsystem top of FIG. 6C.

FIG. 7 illustrates a schematic of the parts of the fluidic circuit inthe assembled cartridge.

FIGS. 8A and 8B illustrate an embodiment of an optical chip for analytetesting.

FIG. 9A illustrates a side cross-sectional view of a portion of thecartridge and optical chip in alignment with an optical scan head of areader device.

FIG. 9B is another view of an end face of a cartridge showing a ledge orlip region protecting the optical chip.

FIG. 10 illustrates the insertion of the cartridge into a reader fortesting.

FIGS. 11A, 11B, and 11C illustrate another embodiment of a fluidcollection device.

FIG. 12A illustrates another embodiment of a fluid collection device.FIG. 12B illustrates an example of how a fluid collection device such asthe one shown in FIG. 12A can be manufactured.

FIGS. 13A, 13B, 13C, 13D, and 13E show an example of an assay useful fordetecting an analyte, such as an analyte from a bodily fluid. FIG. 13Ashows a control sample containing a detectably labeled binding agent(antibody). FIG. 13B shows a test sample reacted with a detectablylabeled binding agent (antibody). FIG. 13C shows antigen attached to asensing site as it appears prior to passing a control sample, such asthe control sample shown in FIG. 13A, across it. FIG. 13D shows antigenon a sensing site and a detectably labeled binding agent (antibody) froma control samples, conjugated to an antigen. FIG. 13E show a sensingsite, such as the site shown in FIG. 13D, after flowing a detectablylabeled sample across the sensing site.

FIG. 14A illustrates kinetics of analyte and antibody binding over time.FIG. 14B shows the kinetics over time of free, unbound antibody bindingto antigen, such as antigen attached to a sensing well.

FIGS. 15A and 15B shows results of an assay signal distribution asdescribed herein for detecting the presence of marijuana (THC;tetrahydrocannabinol) in a sample.

FIGS. 16A and 16B shows results from a multiplex assay as describedherein for detecting cocaine (COC), marijuana (THC;tetrahydrocannabinol) and benzodiazepine (BZO) from a bodily fluidsample.

FIGS. 17A-17C show results from a multiplex assay as described hereinfor detecting cocaine (COC-M), fentanyl (FEN), morphine (MOR) andbenzodiazepine (BZO-O) from a bodily fluid sample.

FIGS. 18A and 18B show part of a microfluidic circuit with a serpentinemixer useful for mixing a sample and a plurality of dried beadscontaining a binding agent.

FIGS. 19A-19B illustrate a method of operating the cartridge (includingan integrated saliva collection system) to test a subject's saliva, asdescribed herein, including both local (e.g., immediate) testing with areader similar to that shown in FIGS. 21A-21B, and confirmation testing.

FIG. 20A shows a partial schematic of an exemplary fluidic circuit forthe cartridge (which may include a saliva collection system), similarthat shown in FIG. 7. FIG. 20B is a legend illustrating component partof the partial schematic.

FIGS. 20C-20N illustrate one example of method of operating an exemplarycartridge for testing a subject's saliva for one or more drugs.

FIGS. 21A-21B show an example of a reader for reading a cartridge andautomatically performing the method of operating the exemplary cartridgeas described herein. FIG. 21A is a front perspective view. FIG. 21B is afront view.

FIG. 21C is a schematic of one example of a reader as described herein.

FIG. 21D shows a front perspective view of one example of a reader (thereader components may be housed within a housing, not shown), includinga cartridge inserted into the reader.

FIG. 21E shows the reader of FIG. 21D, without the cartridge, showingthe slot of the cartridge holder.

FIG. 21F is a back perspective view of the reader device shown in FIG.21D.

FIG. 21G is a side view of the reader device example shown in FIG. 21D.

FIG. 21H is a back view of the reader device example shown in FIG. 21D.

FIG. 21I is a front view of the reader device example shown in FIG. 21D.

FIG. 21J is a top view of the reader device example shown in FIG. 21D.

FIG. 21K is a back view of the reader device example shown in FIG. 21D.

FIG. 21L is a side perspective view of an example of a reader device,showing the gap between the scan head assembly and the back of acartridge when the cartridge is held in the cartridge holder.

FIG. 21M is a closer view of the reader device, showing the back of acartridge (held in the cartridge holder), the gap, and the scan headassembly.

FIG. 21N is another view of the close-up shown in FIG. 21M, with thecover and fiber guide of the scan assembly removed, showing a portion ofthe scan head where the plurality of fibers connected to the lightsources (laser diodes) and sensors (photodetectors) end, across thealignment gap from the photonics ship of the cartridge when a cartridgeis held by the cartridge holder.

FIG. 22 shows an example of an electric field mode profile for photonicchip waveguides.

FIG. 23 shows input coupling efficiency for TE and TM modes.

FIG. 24 shows normalized electric field of TE modes at the3-layer/4-layer (wet) interface.

FIG. 25 shows normalized electric field of TM modes at the3-layer/4-layer (wet) interface.

FIG. 26A shows the results of an optical jump experiment for TE and TMpolarization modes.

FIG. 26B is an example of one variation of a schematic of an opticalreader as described herein.

FIG. 26C is an example of a variation of a schematic for an opticalreader as described herein.

FIG. 27 is an example of a cartridge as described herein.

FIG. 28 is a partial cut-away view of one variations of a cartridgeholder portion of reader apparatus.

FIG. 29 is an illustration of cartridge holder showing a cartridgewithin it.

FIG. 30 is another example of a portion of a cartridge holder includinga cartridge.

FIGS. 31 and 32 show examples illustrating a portion of a cartridgeholder including a ball plunger. FIG. 31 is a top plan view while FIG.32 is a top perspective view.

FIG. 33 schematically illustrates one example of a portion of a reader.

FIG. 34 is an enlarged view of FIG. 33.

FIG. 35 is a top view of a portion of the reader.

FIG. 36 is an example of a cartridge holder portion of a reader.

FIGS. 37 and 38 show linear drive actuator(s) coupled to the cartridgeholder portion of a reader. FIG. 37 is a side view, while 38 is aslightly enlarged view.

FIG. 39 is illustrates one portion of a cartridge holder of a reader,showing thermal regulation (and feedback) that may be helpful

FIGS. 40, 41 and 42 illustrate specific features of an exemplarycartridge that may be used in any of the apparatuses described herein.

DETAILED DESCRIPTION

In general, described herein are reader apparatuses (device and systems)and methods for reading one or more analyte from a photonics chip of acartridge. These apparatuses may be configured to receive one or morecartridges that include a photonics chip.

In general, the methods and apparatuses described herein may be used forthe detection of an analyte (e.g., drug, biomarker, protein, etc.) froma bodily fluid. The examples provided below are directed primarily todetection of an analyte (or multiple analytes) from a saliva sample, andin particular to the detection of one or more drugs of abuse. However,it should be understood that these methods and apparatuses may apply aswell to other bodily fluids and other analytes.

For example, described herein are apparatuses, including opticalreaders, that may be configured to process a cartridge used for salivacollection so that the saliva sample(s) may be prepared for testing todetect one or more analytes. Processing may include regulating themicrofluidics (e.g., combining, mixing, incubating, etc., including inparticular, detection. Analytes may be detected by applying a sensingoptical wavelength to detect a florescent marker in conjunction with aphotonics chip in the cartridge. The reader may control the applicationof the prepared fluid sample onto the photonics chip, and may read outone or more signal(s) to detect and/or quantify signal.

The optical readers described herein may be used with one or morecartridges that can concurrently collect two samples (one for acute orimmediate testing and one for later validation of the acute testing).For example, these cartridges may automatically and accurately process(e.g., dilute) the saliva sample for processing; the optical readerapparatuses described herein may regulate the processing of the fluidsample for detection of one or more analyte. The cartridge may include acap that is pre-loaded with one or more solution (e.g., a dilution fluidand/or a preservation solution). The cartridge may be configured so thatattaching the cap exposes the saliva sample(s) to the appropriatesolution, keeping the different samples isolated from each other, andmay precisely mix and dispense the saliva sample with the dilutionsample in a predictable manner. The cartridge may be configured so thatthe act of snapping the cap onto the body of the cartridge provide themechanical energy for dispensing the dilution fluid, mixing it with thesaliva sample, and dispensing the diluted and mixed saliva dilution intoa diluted sample reservoir (“diluted sample cavity”) where it can befurther processed.

Any of these cartridges may include one or more fluidic circuits thatare configured to processes, in conjunction with a reader, the dilutedsample. The cartridge may include, in communication with the fluidiccircuit or part of the fluidic circuit, a chip (an optical chip, alsoreferred to as a photonic chip) that includes one or more waveguidesalong with detection chemistry that may allow detection via evanescentfield detection of the presence and/or amount of an analyte. Thecartridge may be self-contained, and may include a pump (e.g., adiaphragm, elastomeric membrane, etc.) that may be driven by a driver(e.g., piston, rod, etc.) to push and pull fluid within the microfluidiccircuit. The cartridge may also include a plurality of vents (opening)to atmosphere that may be opened/closed by the reader to control fluidicmovement (including metering, mixing, sampling, etc.) within thecartridge.

FIGS. 1 and 2 illustrate an embodiment of a disposable device 1000 forcollecting, processing, and testing an oral fluid/saliva sample from asubject. After a sample has been collected, the disposable device 1000,which may be a cartridge, can be inserted into a reader for analyzingthe sample. FIG. 1 illustrates the disposable device in an assembledstate, while FIG. 2 illustrates an exploded view of the disposabledevice 1000. In one embodiment, the disposable device 1000 isconstructed as an assembly of a bottom part (cartridge bottom) 100, atop part (cartridge top) 200 and a channel sealing layer 900. In onepreferred embodiment, the sealing layer 900 is a double sided adhesivetape with appropriate cut-outs 902 for fluid conduits/channels that forma fluidic circuit 120. The three parts come together to form a sandwichstructure with the sealing layer 900 in between bottom and top parts100, 200. In one preferred embodiment, the top and bottom parts 100, 200are held together by the double sided adhesive tape.

The sealing layer 900 can be made from a rubber or plastic sheet andheld between the top and bottom part by screws, clips, rivets, bolts, orother fastening mechanisms that can be used to compress the bottom part100 with the bottom part 200. The tightening force applied by the screwsor other fastening mechanism squeezes the rubber or plastic sheet, whichfunctions like a gasket, and provides sealing between fluid channels.

The sealing layer 900 can be made from a rubber sheet and held betweenthe top and bottom part by means of heat staking or mechanical stakingbetween the top and bottom parts. The stakes are designed to provide amechanical force which squeezes the rubber sheet and provides sealingbetween fluid channels.

The bottom and top parts 100, 200 may be connected to each other byapplying liquid adhesive in a pattern required by the fluid channels.The adhesive can also provide sealing between fluid channels.

In some embodiments, the sealing layer 900 can be a combination of thefeatures described above, such as a rubber or plastic layer withadhesives.

In some embodiments, the cartridge top 200 and cartridge bottom 100 maybe hard plastic parts that when assembled form the fluid conduits. Theplastic parts may be manufactured by machining or injection molding orvacuum forming or any other appropriate plastic manufacturingtechniques.

The cartridge top 200 can have an elastomeric membrane 400 covering acut-out in the hard plastic part. The elastomeric membrane 400 may beattached, such as by being glued, to the cartridge top 200. Theelastomeric membrane 400 may be molded over the hard plastic top 200 bymeans of over-molding or two-shot injection molding process. Theelastomeric membrane 400 and the cavity formed by the cut-out can be influid communication with the fluidic channels and can function as a pumpthat drives fluid through the fluidic channels.

FIG. 5C shows another example of the cartridge top (shown from a bottomview, FIG. 5D shows a top view). In this example, the elastomericdiaphragm 400 (pump) is exposed on one side to allow access by thereader piston (not shown). The cartridge top may also include a wasteregion 207 (waste well) and may include calibration regions (e.g.,z-location region 588). The cartridge top also includes an opening 489for the blister pack. FIG. 5D also shown a sample inlet (e.g., which maybe part of the diluted sample cavity/reservoir 201. The cartridge bodymay be made of any appropriate material, for example, a clear,transparent, medical grade polycarbonate (PC) and/or (e.g., overmoldedwith) a medical grade, thermoplastic elastomer (TPE), Shore 40A.

For example, as shown in FIGS. 1, 2, 5A, and 5B, an elastomeric membrane400 can cover a cavity 203 in the cartridge top 200 to create a pumpingwell. The elastomeric membrane 400 may be pushed upon by an actuator ina reader for the disposable device 1000. As the membrane 400 isdepressed into the cavity 203 it pushes the air out of the cavity 203and into the fluid channel. The column of air pushed into the fluidchannel in turn moves a slug of liquid in the fluid channel.

Reversing the direction of motion of the actuator releases the stretchedmembrane 400 which, owing to its elastic nature tries to return to itsoriginal shape and thus tracking the actuator as it moves. As themembrane 400 moves back to its original shape, it creates a suction inthe pumping cavity 203. This suction allows movement of slug of liquidwithin the fluid channel in a direction opposite to the previous motion.Thus, the action of pushing on the membrane 400 and releasing it in acontrolled manner allows bi-directional control over the movement offluid within the fluid channel. As further described below particularlywith respect to FIG. 7, a unique aspect of the disclosed device is themulti-channel management of fluid columns/slugs in the fluidic channelsusing a single on-board pumping mechanism in combination with ventsplaced at strategic locations.

Returning to FIGS. 1 and 2, a blister pack 300, can be assembled withinthe disposable device 1000. The blister pack 300 may contain buffersolution (e.g., control solution) and/or reagents used as part of thetesting protocol. The blister pack 300 may be stuck directly to asealing layer 900 made of double sided adhesive tape. The blister pack300 may be affixed to the cartridge bottom 100 or sealing layer 900 bymeans of an additional double sided adhesive tape placed on the blisterpack 300. The blister pack may be glued to the cartridge bottom 100 orsealing layer 900 by means of a liquid adhesive.

The blister pack 300 can be installed within the disposable device 1000such that it is very close to, proximate to, or adjacent to a piercingmechanism 112, which may be an integral part of the disposable device1000. As shown in FIGS. 2, 4A, and 4B, in one embodiment the piercingmechanism 112 is a sharp pointed feature within the molded cartridgebottom 100. Alternatively, the piercing mechanism 112 may be a sharpneedle that is glued onto the cartridge bottom 100. The needle may bemade from metal or plastic. The piecing mechanism 112 may be press fitor insert molded into the cartridge bottom 100. The piercing mechanism112 can be positioned in a depression within the molded cartridge bottom100 such that the blister pack 300 is positioned above the piercingmechanism 112. The cartridge top 200 may have an opening 113 thatprovides access to the blister pack 300 and allows an actuator of thereader to push the blister pack 300 into the piercing mechanism andthereby release the contents of the blister pack into the fluidchannels.

As shown in FIGS. 1, 2, and 5B, the disposable device 1000 can alsoinclude a sensing element 3000 in fluid communication with the fluidiccircuit 120. The sensing element 3000 may be a photonic chip which isplaced within a cavity 204 in the cartridge top 200. The sensing element3000 may be held in place by being sandwiched between the cartridge top200 and cartridge bottom 100 and can be held together by means of anadhesive sealing layer 900, for example.

In one embodiment as shown in FIGS. 1 and 2, the disposable device 1000has an integrated collection device and cartridge. The cartridgeincludes primarily the cartridge bottom 100, the cartridge top 200, andthe associated components as described herein. The collection deviceincludes primarily a pair of collection swabs 610, 620 and a cap 500 andassociated components as further described herein.

As shown in FIGS. 1, 2, 3A, and 3B, first and second swabs 610, 620 canbe held firmly within first and second swab holders (e.g., swab pistons)710, 720 respectively. The swab holder may alternatively be referred toas swab pistons. The swabs 610, 620 may be held within swab holder 710,720 by means of press fit. Alternatively, the swabs 610, 620 may also beglued to the swab holders 710, 720. The saliva collection swabs 610, 620may be made of an absorbent material, such as a sintered porous polymerwith an open cell foam structure similar to one used in wicks. Othermaterials that can be used include polyurethane foam or cellulose fiber.At least one of the saliva collection swabs 610, 620 may have anembedded indicator, such as a colored dye indicator, which changes colorupon contact with oral fluids thus indicating completion of the salivacollection. A saliva stimulant configured to stimulate saliva productionfrom a subject may be included on first and/or second collection swabs610, 620 or otherwise administered to a subject. Since confirmatorytesting by the certified lab typically uses traditional testing systemsand protocols, a larger amount of saliva may be collected for theconfirmatory sample, such as about 2, 3, or 4 times the amount ascompared for the rapid test sample. Therefore, in some embodiments, theindicator is included with the confirmatory saliva collection swab 620.In one embodiment the rapid test saliva collection swab 610 is designedto be a hollow shell. The amount of oral fluid collected can becontrolled by the size of the collection swabs 610, 620 and the positionof the indicator on and/or within the swabs. FIGS. 11A, 11B, and 11Cshow another embodiment of a collection swab. First collection swabs610′ may have a structure including a plurality of capillary channels614. (A second collection swab as used herein may have a generallysimilar structure as a first collection swab with the most commondifference a matter of size or dimensions). Upon placing first capillarycollection swab 610′ in the mouth of the subject (e.g., under thesubject's tongue), capillary channels 614 absorb the oral fluid bycapillary action and collect only as much as the channel volume allowsthem.

FIGS. 4D and 4E illustrate one example of a collection body 455. Thecollection body may be flanged outwards and may mate with cartridge (notvisible in FIG. 4) body. In some variations the collection body may bethe same or integral with the cartridge body. In FIG. 4D the collectionbody includes a connector 457 (a female portion of a snap fit in thisexample) for connecting to the cap. A pair of swab pistons 710 extenddistally from the collection body. Each swab piston includes an internalchannel 458 configured to wick saliva from an open distal end of thefirst swab piston. For example the channel may hold a porous materialand/or capillaries. The swab pistons may each also include a seal (e.g.,plunger seal) 459. FIG. 4E shows an internal view of the collectionbody, showing a connection within the body for fluidic connection to thecartridge portion (e.g., the diluted sample cavity in the cartridge). Inthis example, the collection body includes a male lure 462 connectionfor connecting to the cartridge.

The collection body and/or swab pistons may be made of any appropriatematerial, for example, a clear, transparent, medical grade polycarbonate(PC) and/or (e.g., overmolded with) a medical grade, thermoplasticelastomer (TPE), Shore 40A.

As mentioned, the wicking material within the swab piston, which may bereferred to as the swab, may be porous material and/or it may beconstructed by putting a number of capillaries 616 together in a bundlewith a sheath 612 around them to hold them together or for protection.Such capillaries may be curved or otherwise shaped, but in general willbe straight. Alternately a swab may be constructed using a multi-lumencapillary with the requisite number of lumens. The capillaries may bemade of glass or plastic material or otherwise manufactured or treatedto minimize binding of substances of interest to prevent their lossprior to assay. A swab may be relatively rigid or may be flexible to aidin placement. A swab may have a flat end(s) or may have one or moreshaped end 618 as shown in FIG. 11A which may allow easy access tosaliva for capillary suction upon placing the swab in the mouth (e.g.,under the tongue). An entire swab or swab holder may be shaped to aid incollection and/or handling. Such a shaped end or shaped swab may beflattened, rounded, tapered or so on. Although the capillaries orchannel may all be the same length, in some examples, some capillariesor some channels may be shorter than others. For example, capillaries onone side of a taper may be shorter than capillaries on the other side ofthe taper. Likewise, a swab with a single channel in a hollow shell or aporous material may have different dimensions on different parts, andone longitudinal part of a channel, shell or single material swab may belonger than another part (e.g., 1%-50% longer). FIG. 11C shows a crosssection through a swab showing one example of placement of capillaries.

FIGS. 12A and 12B illustrate swab 610″ with a plurality of channelsconfigured to collect a bodily fluid. FIG. 12A shows a perspective viewand FIG. 12B shows a front view of the three sections of a swab beforeand after joining the sections. A swab may be made in a sandwichconstruction whereby two or more halves or parts of a swab come togetherto create capillary channels. Each half or part may be made of amaterial with channels cut out as shown in FIG. 12B. In someembodiments, an opening (channel) is cut out of one half or part, andthe floor or roof of the channel is supplied by another half of part ofthe swab. In FIG. 12B, top section 622 of swab 610′ houses top channels628 while middle section 624 of swab 610′ provides floors 632 for topchannels 628 when the top section 622 and middle section 624 of the swabare adjoined. Top 622 of swab 610′ also provides roof 634 for middlechannels 630 provided by middle section 624. Similarly, middle section624 and bottom section 626 also form channels. In some embodiments, acut out channel is half a channel and two half channels come together tocreate a complete capillary channel(s) (as could be seen if top section622 and middle section 624 were offset from one another. Channels may beany shape that collects or transports the body fluid, such as circular,rectangular, rounded rectangles and so on. Halves or parts may beplastic and the plastic parts may be manufactured by machining orinjection molding or vacuum forming or any other appropriate plasticmanufacturing techniques. The plastic parts may be joined together bypressure sensitive adhesive or liquid adhesive or by ultrasonic weldingor any other plastic joining techniques known in the art.

A swab may have at least 2, at least 3, at least 4, at least 5, at least10, at least 15, at least 20, or at least 30 channels. In some preferredembodiments, a swab may have between 14 and 22 channels, such as about18 capillary channels. Capillary channel(s) of a swab may have a lengthbetween 1 mm and 10 cm and in general will have length between 5 mm and50 mm (5 cm). In some embodiments, a capillary, a capillary channel, ahollow shell or a porous material has a length of from 5 mm to 40 mm,such as approximately 25 mm (from 10 mm to 25 mm). Each capillarychannel or lumen may have a diameter between 0.05 mm and 5 mm, such asbetween 0.1 mm and 1.5 mm (e.g., between 0.3 mm and 0.8 mm.) In general,a length of capillary selected is less than the capillary head for theselected diameter. That is, for a selected capillary channel diameter,the length of oral fluid pulled into the channel due to capillary actionagainst gravity is greater than the selected length of the capillarychannel to ensure consistent collection volume.

Saliva Collection

In some examples, a pair of saliva samples are collected simultaneouslyby placing the saliva collection swabs 610, 620 in the mouth of the testsubject. The saliva collection swabs 610, 620 may be sized, shaped, anddesigned ergonomically to be placed under the tongue on either side ofthe tongue. This may enhance the salivation of the test subject andallow for improved collection efficiency. In some examples, a salivacollection swab may be configured for increasing saliva production, suchas allowing or encouraging biting or chewing or may contain a componentconfigured to increase saliva production such as a chemical or odorant.In some examples, components for increasing saliva production may beseparate from a collection device, such as a separate vial containing anodorant, etc. In some examples, a single saliva sample may be collectedsuch as a single sample in which part of the sample is used for rapidtest analysis and another part used for confirmatory testing. In someexamples, two or more saliva samples may be separately collected (e.g.,using two or more separate collection devices).

One of the saliva collection swabs 610 is used for the rapid testperformed within the cartridge portion of the disposable device 1000,while the saliva sample collected by the other swab 620 may be used fortesting by a certified forensic lab for confirmatory testing and/or canalso be used for storage as forensic evidence.

Once the saliva/oral fluid is successfully collected by the salivacollection swabs 610, 620, the user applies the collection device cap500 over the oral fluid collection end, i.e. the saliva collection swabs610, 620, of the disposable device 1000.

As shown in FIGS. 6A and 6B, the collection device cap 500 has twocavities 501, 502 to receive the saliva collection swabs 610, 620. Insome embodiments, the disposable device can have more than 2 collectionswabs, such as 3, 4, or 5 swabs, and the device cap 500 can have amatching number of cavities. The rapid test cavity 501 is filled with aknown amount of dilution buffer solution used for dilution of the rapidtest saliva sample collected by swab 610. The dilution buffer solutionmay be constituted of 5% bovine serum albumin (BSA) in phosphatebuffered saline (PBS), for example. Other concentrations of BSA or otherprotein can be used, such as between 2-10%. In addition, other proteinsmay be used in the dilution buffer solution, such as non-fat dry milk,and other buffers can be used, such as tris-buffered saline (TBS). Theconfirmatory test cavity 502 is filled with a preservation solution usedto preserve the confirmatory sample collected by swab 620 so that theconfirmatory sample can be sent to a certified lab for confirmatorytesting. The preservation solution may include a buffer.

The two cavities 501, 502 filled with dilution and preservation fluidsrespectively may be sealed by means of a foil cover 510 or otherremovable or pierceable sealing mechanism, such as a lid or cap. Theprimary purpose of the foil cover 510 is to contain the dilution andpreservation fluids within the collection device cap 500. The foil cover510 is designed to have very low vapor permeability to prevent orgreatly reduce any ingress of water vapor and any evaporation of thefluids within the cavities 501, 502. The foil cover may be a heatsealable foil with a typical multi-laminate construction of a layer ofaluminum foil for reduced vapor permeability, and a polymer layer (forexample polypropylene) for heat seal ability.

Upon connecting the collection device cap 500 with the cartridge of thedisposable device 1000, the collection swabs 610, 620 pierce through thefoil seal 510 within the cap 500 and move into the cavities 501, 502.The action of closing the collection device cap 500 generally xinitiates the sequence for dilution of the saliva sample for rapidtesting.

FIGS. 6C-6D show additional examples of a cap. FIG. 6C shows a sectionview (bisecting the cap in the long axis) shown in the inside of thecap. In this example, the frangible cover (shown as a foil seal 698)enclosed the fluid held within the tubes of the cap. For example, thefirst tube 678 includes a dilution buffer (rapid test buffer) 679, whilethe second tube 668 includes a preservation solution (lab test buffer)669. FIG. 6D shows an external view of this variation of a cap, showingconnector (e.g., a male snap-fit connector 699) that may click and lockonto the collection body, as described. In some variations the connectoris configured to snap on with a force sufficient to drive fluid from thetubes in the top, through the swab piston, mixing, and dispensing intothe diluted sample cavity.

As shown in FIGS. 1 and 2, the swab holder 710 is sized, shaped, anddesigned to act as a plunger within the cavity 501 of the collectiondevice cap 500. The O-ring 730 fitted onto the swab holder 710 providesa fluid seal between the swab holder 710 and cavity 501 during theplunging action, which ensures that the displaced dilution buffersolution is forced through the collection swab 610 to mix with thecollected saliva sample.

The O-ring may be an over-molded elastomeric lip type feature to providethe sealing function. The elastomer can be silicone, thermoplasticelastomer (TPE) or any other elastomeric material that does not causeany contamination of saliva/oral fluid sample by means of chemicalreaction or leaching chemicals or absorption of analyte.

As shown in FIGS. 1, 2, 4B, 5A, and 5B, the swab holder 710 has a fluidpathway 111 connecting the back end of the porous saliva collection swab610 to a diluted sample cavity 201 within the cartridge. The dilutedsample cavity 201 holds the diluted sample within the cartridge forfurther use in the rapid test.

As the cap 500 is closed, the swab holder 710 performs a plungingaction. The plunging action pushes upon the dilution buffer fluid withinthe cavity 501. As the cavity is sealed by the O-ring 730, the dilutionbuffer within the cavity 501 is forced through the porous salivacollection swab 610 and into the diluted sample cavity 201 within thecartridge through the fluid pathway 111. As the dilution buffer movesthrough the saliva collection swab 610, it mixes with the saliva samplecontained within the porous swab 610.

A dilution factor can be defined as:

Dilution Factor(DF)=(Plunged Volume)/(Volume of Saliva)

The volume of saliva collected depends on the porosity or open space ofthe saliva swab material and the solid volume of the saliva swab 610,and if used, the location of the fluid indicator on the swab. Ingeneral, for a given shape, size and material the maximum or desiredvolume of saliva collected by the swab 610 is generally fixed. Forexample, the volume of saliva collected depends on the overalldimensions. For example, the capillary volume within saliva swab 610 is:Capillary Volume=No. of Capillaries×Length of Capillary×Cross-sectionArea of Capillary. The volume of saliva obtained by a swab may bebetween 3.0×10-5 mls to 3 mls. In some particular examples, the volumeof saliva obtained by a swab is between 0.01 mls and 1.0 ml (e.g.,between 0.1 mls and 1.0 mls).

The amount of fluid pushed through the swab is equal to the volumeplunged by the swab holder 710. The dilution factor therefore isdependent only on geometry and material selected. Thus the devicedisclosed can achieve a very consistent dilution factor. Any variabilityin the dilution factor is directly controlled by the manufacturingtolerances of the swab 610, and the swab holder 710. The dilution factormay also be measured and calculated by including a known quantity orconcentration of a substance in the dilution buffer which is thencombined with the saliva sample and tested along with the analyte ofinterest. The dilution factor can be equal to the known concentration ofthe substance in the dilution buffer divided by tested concentration ofthe substance after combination with the saliva sample.

The diluted sample pushed through the swab 610 is collected in thediluted sample cavity 201 within the cartridge. The cavity 201 can beprovided with a capillary stop valve 101 to prevent the sample frommoving into the fluidic circuit by capillary action.

The collection device cap 500 may then be connected to the cartridge bymechanical means. The mechanical connecting means may be a snap fitmechanism to hold the cap in place. Additionally, the mechanicalconnection can be a single use snap fit that can be designed in a mannersuch that it cannot be opened without permanently damaging the snap fitmechanism thus preventing any possibility of tampering.

Once the cap 500 is placed firmly, the disposable device 1000 may beinserted into a reader 1002 for automated testing as shown in FIG. 10.

The reader module 1002 receives the disposable device 1000 and clamps itin place. As the detection system is an optical sensing system, thedisposable device 1000 needs to be accurately located within thecartridge and/or accurately aligned with the optical sensing mechanismin the reader 1002. For this purpose, the disposable device 1000 has twofeatures that ensure accurate alignment of the device within the readermodule.

Any of the apparatuses (e.g., readers) described herein may include az-alignment feature. With the disposable device 1000 clamped within thereader module, as shown in FIG. 9A, the front face 3102 of the photonicchip may be excited by an optical element within the reader. The opticalelement within the reader may also sense the photonic informationemitted from the photonic chip.

A Z-gap 1006 can be defined as the distance between the front face 3102of the photonic chip 3000 and the sensing element 1004 within the readermodule. This Z-gap is helpful for accurate excitation and sensing of thephotonic chip 3000 as the intensity of light transferred between thechip and the sensing element may vary with the square of the Z-gap.

As shown in FIGS. 1, 2, 5A, 5B, and 10, upon insertion of the disposabledevice 1000 within a reader 1002, the face 212 of the cut-out feature208 butts against a dowel pin 1008 present in the reader 1002. The face3102 then becomes a reference face for location of all fluidic featuresand the chip cavity 204 that holds the photonic chip 3000.

With a pre-designed reference face 212 engaging with a pin 1008 in thereader module 1002, the Z-gap 1006 can be accurately controlled and anycartridge-to-cartridge variation of the Z-gap 1006 can be kept within acontrolled narrow band.

Z-gap variability may dependent on the tolerance stack-up of featureswithin the disposable device 1000 and may be controlled by themanufacturing process.

Any of the apparatuses described herein may include an optical sealingfeature. As shown in FIGS. 8A, 8B, and 9 (showing examples of photonicchips that may be used in a cartridge as described herein), the sensingmethod may involve a laser illumination of the photonic chip 3000 bymeans of an optical scan head 1004 within the reader. The scan head 1004shines a laser which is received by an optical waveguide 3103 within thechip 3000. In FIG. 8A, there are four excitation-receiving waveguides3121 that intersect with eight detection (or emission) waveguides 3123(an additional loopback waveguide is also included); a well is locatedat each intersection. The light irradiates the sensing wells 3101 withinthe chip 3000. These wells have coated reagents, such as antigens of theanalytes being tested, which bind with the binding agents (fluorophoreconjugated antibodies) added to the sample. The analyte/sensing wells(also called sensing sites) can be pre-conditioned with antigens. Anantigen can be bound to a sensing well using any type of tether, such asBSA, another antibody, etc. In some embodiments, the amount of boundantigen in the sensing well 3101 is much greater, such as on the orderof at least 10, 100, or 1000 times (e.g. mole per mole) the amount offluorophore conjugated antibody that is added to the control sample andoptionally also the saliva sample. This ensures that the antibodies fromthe control sample only uses up a very small fraction of the antigen,which can essentially or approximately considered to be an infiniteamount relative to the amount of antibody, which means that there issufficient amount of free antigen to process the saliva sample withoutwashing the sensing wells 3101 to remove the antibody bound to theantigen. The saliva sample may generate a higher fluorescent intensitydue to control antibodies left in the well, but this offset can beaccounted for, subtracted out, or ignored by measuring the slope of thefluorescent intensity as a function of time. FIG. 13D shows sensingwells 818 with attached antigen 822, for example a drug attached to asensing well via tether 820 such as a BSA (bovine serum albumin)attachment molecule. Detectably labeled antibody from the control samplehas attached to antigen (see the far right of FIG. 13D). Upon theaddition of a reacted sample (e.g., a diluted bodily fluid sampleincubated with a detectably labeled antibody), unbound antibody willbind to available antigen (see the far left of FIG. 13E) and increase insignal intensity of the sample can be measured over time. As indicatedabove, FIG. 14B shows the kinetics over time of free, unbound antibodybinding to antigen, such as antigen attached to a sensing well. Theslope is determined by the diffusion coefficient of the unbound antibodyin contacting and binding to the antigen (drug) bound to the well. Thetop part of FIG. 14A shows the equilibrium between analyte found in asample binding to antibody (thus preventing such antibody from bindingto antigen in a sensing well). The bottom part of FIG. 14A shows theequilibrium between detectably labeled antibody and antigen in a sensingwell.

The sample metering well 102 may include lyophilized beads havingantibodies conjugated with fluorophores that absorb the incoming laserlight and then re-emit at a known wavelength. The re-emitted light fromthe fluorophores is recoupled into another set of waveguides 3103 whichdirect the light from the fluorophores back to the front face 3102 ofthe chip 3000. The re-emitted light by the fluorophores received withinthe waveguides 3103 is measured by the optical scan head 1004 and is thetrue measure within the system.

This re-emitted light from the fluorophores can also couple optically tothe fluid (sample or control) in contact with the photonic chip 3000.Such light can then be dispersed into the medium and reach the frontface 3102 of the cartridge and can also be picked up by the scan head1004 along with the light within the sensing waveguides 3103 of thechip. This light may become a major source of error in measurement ifnot dealt with.

Two key pathways of this ‘optical leakage’ were identified: (1) thetransmission of light through the material of the cartridge bottom 100,and (2) the transmission of light through the double sided adhesive tape900. To address the optical leakage, the cartridge bottom 100 is madefrom an opaque material (preferably black polycarbonate).

As shown in FIG. 9A, to block the optical leakage through the doublesided adhesive 900, a ledge feature 110 or lip may be provided at thefront end of the cartridge bottom 100. The double sided adhesive 900 isplaced behind the ledge 110 such that the ledge 110 is between thedouble sided adhesive 900 and the optical scan head 1004. The height ofthe ledge 110 is designed such that the double sided adhesive 900 iscompletely recessed post compression within the sandwich structure ofthe assembled disposable device 1000. FIG. 9B illustrates another viewof a distal end region of a cartridge portion that may integrated with asaliva collection system, the end including a ledge or lip region 110.

Thus the front edge of the cartridge bottom 1000 becomes entirely opaqueand provides proper optical sealing and may eliminates a major source oferror in measurements.

FIG. 7 is a schematic that illustrates how fluid is transported throughthe fluid channels in the cartridge using a pump 400 and a series ofstrategically placed vents V1, V2, and V3 and capillary stops 101, 104,and 108. Vent V1 is positioned downstream of the waste well 207. Vent V2is positioned upstream the sample metering well 102 and downstream thediluted sample cavity 201, i.e. between the sample well 102 and thediluted sample cavity 201. Vent V3 vents and leads to the diluted samplecavity 201. A first capillary stop 101 is located just downstream thediluted sample cavity 201. A second capillary stop 104 is locateddownstream of the mixer 103 for the sample metering well 102 andupstream of the chip 3000. A third capillary stop 108 is locateddownstream the mixer 107 for the control metering well 106 and upstreamthe chip 3000. The diluted sample is received in a chamber (dilutedsample cavity) 201 and is retained within the chamber by means of acapillary stop 101. The capillary stops prevent the fluid from advancingthrough the fluid channels by capillary action. Advancing past thecapillary stops generally requires application of the pump. Thedisposable device has three vent holes V1, V2, and V3. Upon insertion ofthe disposable device in the reader, the reader establishes establishfluidic connection with the vent holes. The vent holes are in fluidicconnection with valves within the reader. These valves allow the readerto open or close the vents as required.

The valves may be solenoid operated plunger type valves or pinch valvesor air operated piston valves, for example.

At the start of the test and/or initialization sequence, the vent valveV1 is open to atmosphere and thus allows venting of the waste channel114. At the same time, vents V2 and V3 are kept in closed position thussealing off all other channels.

The pump membrane 400 is pushed down to remove air from the pumpingchamber. With vent V1 in open position and V2, V3 in closed position,the air escapes through V1 without affecting the sample contained withinthe diluted sample cavity 201. This primes the pump 400 for a suctionoperation. Next, vent V3 is opened and V1, V2 are closed. This allowsthe pump to move fluid in the diluted sample cavity 201. The pumpactuator in the reader gradually releases the pump membrane 400 therebycreating suction in the fluid channels. Due the suction, the dilutedsample moves past the capillary stop 101 and into the sample meteringwell 102. A fluid sensor FS1 positioned at the end of the samplemetering well 102 senses the presence of fluid (sample) in its viewfield and the control unit of the reader stops the movement of the pumpactuator and the pump membrane 400 and thus stopping the movement ofdiluted sample in the sample metering well 102 after it has filled thesampled metering well 102.

Fluid sensors FS1 and FS2 may be non-contact optical reflectance ortransmission type sensors as part of the reader.

Next, vent V2 is opened and V1, V3 are closed. The pump actuator thenfurther releases the pump membrane 400 to further pull the dilutedsample into the mixing chamber 103. At this time, air is pulled into thecartridge through the vent V2, which ‘cleaves’ off a slug of the dilutedliquid sample present in the sample fluid channel. The air thus isolatesa slug of diluted saliva sample of a known volume within the samplemetering well 102, thereby providing a controlled and metered volume ofsample for testing.

Additionally, the sample metering well 102 may contain solid reagentsthat modify the diluted saliva sample as a part of the assay for analytedetection within the saliva sample. In one embodiment, these reagentsare in the form of a freeze dried/lyophilised bead(s) that may includeantibodies conjugated with a fluorophore and sugars or other stabilizersfor stability. The bead(s) may be placed within the sample metering well102 of the cartridge during assembly of the disposable device. Thereagents may be in the form of multiple small pellets or powder form forimproved dissolution. The surface of the sample metering well 102 may bespray coated with the reagents to allow better distribution of thedissolved regent within the slug of diluted saliva sample.

The lyophilised bead or other material containing the reagent dissolvesupon contact with the diluted saliva sample. Owing to the lowdiffusivity of proteins within saliva, the dissolved reagents typicallycreate a high concentration zone within the slug of saliva sample. Foraccurate testing, the reagents need to be uniformly dissolved within theentire volume of metered sample.

Uniform distribution of reagents within the saliva sample is achieved bypassing the saliva sample through a mixing chamber 103.

Mixer Operation

The mixing chamber 103 is a passive microfluidic mixer which improvesthe concentration distribution of the dissolved reagents within themetered slug of the diluted sample.

In the disposable device disclosed herein, the mixing chamber 103achieves mixing by manipulating the fluid flow to enhance the chaoticadvection.

In one preferred embodiment the mixer 103 is a serpentine channel whichutilizes the variation of speed of fluid around the bends of the samplefluid channel. This difference in speed of fluid between the inside andoutside radius of the bend of the serpentine channel creates advectionwithin the cross section of flow. As the fluid moves along thealternating bends of the serpentine channel, the chaotic advectionincreases and thus enhances mixing. In some embodiments, the fluidicchannels, and in particular one or more serpentine channels have aninner diameter of at least 50 um, at least 100 um, or at least 500 um.Such channels may be readily formed using less expensive moldingtechniques and/or may allow better mixing, particularly during the backand forth movement and movement around any curves in the channels.

The pump actuation continues to release the pump membrane to pull themetered sample into the mixing chamber 103 and then stops. To reduce thelength of channel required for mixing, a multi pass approach may beapplied. The pump actuation is reversed and the pump membrane 400 ispushed down to move the metered saliva sample back into the samplemetering well 102. The pump actuation is again reversed to pull thesample back into the mixing chamber 103. This process can be repeatedmultiple times to increase the mixing. FIGS. 18A and 18B showsconcentration maps for a fluidic circuit with a serpentine channel and asample well. FIG. 18A shows a simplified view and FIG. 18B shows anexpanded view of a fluidic circuit 120 with a serpentine channel andsample well 102 for mixing a sample. Sample well 102 contains beads 800with reagent, e.g. detectably labeled antibody. Diluted bodily fluidenters sample well 102 from diluted sample cavity 201, diluting anddissolving beads 800, forming metered sample. The scales on the rightindicates reagent concentration (e.g., detectably labeled antibody) indifferent shades. The highest concentration is in the beads as shown bythe dark color. As fluid moves along the alternating bends of theserpentine channel and back and forth between the serpentine channelsand even into the sample well, reagent concentration becomes moreconsistent. In one embodiment, a relatively uniform distribution wasachieved within 3-7 passes of the sample through the mixing chamber 103.

In a Split and Recombine (SAR) configuration, the fluid channel splitsinto two or more separate channels and then recombine into a singlechannel, or a 3-Dimensional Serpentine configuration with cross ridges.

For microfluidic flow, the Reynolds number is typically <1 and hence,diffusion is the dominant mode for mixing of fluids. Typically, assayreagents are small proteins and have low diffusivity in saliva. Inaddition, diffusion is a very slow process which makes it difficult tomix fluids at microfluidic scales.

Microfluidic mixing schemes can be either “active”, where an externalenergy or force is applied to perturb the sample species (e.g., a mixingpaddle, etc.), or “passive”, where the contact area and contact time ofthe species samples are increased through specially-designedmicrochannel configurations.

For a disposable device, active mixing introduces many problemsincluding complicated fabrication, increased cost etc. Passivemicromixers contain no moving parts and require no energy input otherthan the pressure head used to drive the fluid flows at a constant rate.Due to the laminar characteristics of micro-scaled flows (Reynolds <1),mixing in passive micromixers relies predominantly on chaotic advection.

After the mixing step the sample is held within the mixing chamber 103.The capillary stop 104 at the exit of the mixing chamber prevents anymovement of sample past the capillary stop 104 due to capillary action.

The vent V1 is then opened and V2, V3 are closed. At this point theblister actuator within the reader pushes down on the blister pack 300.The actuator pushes down on the blister pack 300 in controlled stepstill the blister bursts and releases the control fluid out of theblister pack 300 and into the control fluid channel.

The blister actuator pushes further on to the blister pack 300 to pushthe control fluid into the control metering well 106. A fluid sensor FS2positioned at the end of the control metering well 106 senses thepresence of the control fluid in its view field when the controlmetering well 106 has been filled and the control unit of the readerstops the movement of the blister actuator and thus stopping themovement of control fluid in the control metering well 106.

The pump actuator then pushes down on the pump membrane 400. Since thepump is located upstream the control metering well 106, this pushes airinto the control fluid channel which ‘cleaves’ off a slug of the controlfluid present in the control fluid channel and control metering well106. The air thus isolates a slug of control fluid of a known volumewithin the control metering 106, thereby providing a controlled andmetered volume of control fluid for measurements.

Additionally, the control metering well 106 may contain solid reagentsthat modify the control fluid as a part of the assaymeasurements/testing. In the preferred embodiment, these reagents are inthe form of a freeze dried/lyophilised bead(s). The bead(s) may beplaced within the control metering well 106 of the cartridge duringassembly of the disposable device.

The reagents may be in the form of multiple small pellets or powder formsuch as for improved dissolution. A control reagent may include one or aplurality of types of control reagents. Such reagents may be in a singlebead, pellet, powder or other form, or may be in a plurality of beads,pellets, powders or other forms or a combination (e.g., one controlreagent in a bead, another control reagent in a powder, etc.). A controlreagent may be an antibody or other molecule configured to bind to asubstance of interest (e.g., a drug, a legal substance, an illegalsubstance, a metabolite of such substances and so on). Two or morecontrol reagents may be used to assay a single substance such as byusing a first control reagent to detect a substance of interest andusing a second control reagent to detect a metabolite (or differentepitope or part) of a substance of interest.

The surface of the control metering well 106 may be spray coated withthe reagents to allow better distribution of the dissolved regent withinthe slug of control fluid.

The lyophilized bead containing the reagent dissolves upon contact withthe control fluid. For accurate testing, the reagents need to beuniformly dissolved within the entire volume of the metered controlfluid.

Uniform distribution of reagents within the control fluid may beachieved by passing the control fluid through a mixing chamber 107. Themixing method is the same as described for the diluted saliva sample.

After the mixing step in some examples the control fluid may be heldwithin the mixing chamber 107. The capillary stop 108 at the exit of themixing chamber 107 prevents any movement of the control fluid past thecapillary stop 108 due to capillary action. In other examples, thecontrol fluid may be moved out of mixing chamber 107 immediately aftermixing and into chip channel 109 for assay.

At this point, at least the sample fluid or both the sample and controlfluids are held stationary within the respective mixing chambers for afixed duration (typically 5-10 minutes). This allows for antibodies tobind with the analyte in the sample. FIG. 14A illustrates the kineticsof antibody binding with analyte in the sample during the sampleincubation phase.

After incubation of the sample and control fluids, the pump actuatorpushes down on the pump membrane 400 to move the control fluid out ofthe mixing chamber 107 and into the chip channel 109. The pump actuatorpushes down on the membrane 400 a known amount which in turn moves thecontrol fluid a known distance within the chip channel 109. The controlfluid is stopped at a point in the chip channel 109 such that thecontrol fluid covers the entire sensing area of the chip 3000. At thispoint optical measurements are made to sense the analyte reaction withinthe control fluid.

Post-measurement, the entire metered volume of control fluid is pushedfurther into the waste well 207. The selected chip channel and pumpvolume ensures that the entire chip channel 109 is empty after pushingthe control fluid into the waste well 207.

Next, vent V2 is opened and V1, V3 are closed. The pump actuator thenmoves in reverse direction to release the pump membrane 400 and createsuction within the sample fluid channel. This moves the incubated sampleout of the mixing chamber 103 and into the chip channel 109. The fluidis moved a known amount such that the metered volume of the incubatedsample covers the entire sensing area of the chip 3000. Opticalmeasurements are made to sense the analyte reaction within the salivasample.

Upon completion of measurements, the pump is released completely. Thismoves the saliva sample out of the chip channel 109 and into the controlfluid channel which now functions as a secondary waste well. Since manytests only require the detection of a threshold amount of the analytesuch as a drug, a single control sample having the analyte at thethreshold concentration is sufficient to establish whether the salivasample has a concentration of analyte that is greater than, less than,or equal to the threshold concentration. A readout to a user in such acase may indicate “Pass” or “Not detected” or “Fail” or “Detected or“Error” or the like. If an absolute concentration of the analyte isdesired instead, multiple blister packs having varying concentrations ofthe analyte of interest can be added to the cartridge and tested toconstruct a calibration curve.

The reader may coordinate and control (e.g., using a controllercomprising one or more processors) the operation of the vents (e.g.,opening, closing), the pressure (increase, release, hold) on the pump(pumping membrane), the scan head, etc.

As indicated above, included herein is a method for analyzing a bodilyfluid from a subject. A bodily fluid may be analyzed for detecting forone or more than one substances of interest (analytes), such as 2, 3, 4,5, or more than 5 substances of interest. The method may include thesteps obtaining or having obtained a bodily fluid sample from a subject,the sample suspected of containing a first analyte. Although any bodilyfluid (or biofluid) such as blood, breast milk, plasma, sweat, tears,urine, etc., may be used, in general the method uses an oral fluid suchas a saliva sample that may readily be obtained non-invasively andwithout requiring any special facilities such as a lab or bathroom. Sucha fluid may be readily obtained from a subject by a person having nomedical training and no or very little special training. FIGS. 13A-13Eshow how a method for analyzing a body fluid from a subject for asubstance of interest.

A method as described herein may include the steps of mixing the bodilyfluid sample with a first detection reagent comprising a first aliquotof a first binding agent. In general a first binding agent will includeor contain or will bind to a detectable label. A first detection reagentmay include a plurality of binding agents (second, third, fourth, etc.).A detectable label associated with a binding agent may include a labeldetectable by a reader using a laser and evanescent sensing. One or morethan one types of detectable labels may be used. For example, detectionof each of a plurality of analytes may use different detectable labelssuch that each analyte may be analyzed. In some examples, two or moreanalytes may use the same label. For example, a binding agent for twodifferent opioids may use the same label such that a bodily sample canbe determined to have more than an acceptable amount of “opioid”. Insome examples, a first (second, third, etc.) binding agent is adetectably labeled antibody configured to bind a substance of interest(first analyte, second analyte, third analyte, etc.) in the bodilysample to generate a sample mixture. A label may be a fluorophoreattached to or configured to be attached to an antibody. A method asdescribed herein may include a step of incubating the sample mixtureunder conditions configured to bind first analyte (second analyte, thirdanalyte, etc.) to the first binding agent (detectably labeled antibody;second binding agent, third binding agent, etc.) to generate a reactedsample from the subject wherein first (second, third, etc.) detectablylabeled antibody that is not bound to first analyte (second, third) hasan available epitope. The amount of antibody may be in excess ofanalyte. In other words, only some of the available antibody may bebound to analyte. A method as described herein may include providing afirst control sample comprising a first control aliquot of first(second, third, etc.) binding agent. A binding agent may be one or moredetectably labeled antibodies wherein the antibodies are not bound to anantigen or analytes and have an available epitope. Such a first controlaliquot may include a plurality of antibodies, which may be initially befound in a test device as non-aqueous or lyophilized or dried as beads,pellets, sprays, etc. and may be located in control metering well 106 asdescribed elsewhere herein and may be reconstituted using solution fromblister pack 105. A non-aqueous or lyophilized or dried beads, coating,pellets, sprays, etc. may contain a single binding agent or may containa plurality of binding agents. For example, a single dried bead,coating, pellet, spray may contain just 1 binding agent or may contain2, 3, 4, 5, or more binding agents. Alternatively, a system as describedherein may include a plurality of dried beads, coatings, pellets, orsprays and such each one may include only a single binding agent or onlya subset of binding agents. A particular delivery form for bindingagent(s) may be chosen for cost or ease of manufacturability, ease orspeed of reconstitution or so on. A first control sample may include aone or more than one detectably labeled binding agents. A method foranalyzing a bodily fluid as described herein may include the step ofproviding at least one analyte sensing site having a supply of firstantigen (second antigen, third antigen, etc.) attached thereto. At leastone analyte sensing site may include 1 or more (2, 3, 4, 5, 10, 20 ormore or anything between these numbers) of analyte sensing sites such asanalyte sensing sites 3103 shown in FIG. 8B. A method for analyzing abodily fluid as described herein may include the steps of passing thefirst control sample over the at least one sensing site to therebyconjugate first binding agent (detectably labeled antibody) to the first(second, third, etc.) antigen in the at least one sensing site andthereby activate a first (second, third, etc.) detectable controlsignal.

A method for analyzing a bodily fluid from a subject may also includethe step of after the passing the first control sample step, measuringover time detectable signal from the at least one sensing site togenerate a first set of measurements. Such measurements may be takenover time from the same at least one sensing site. As shown in FIG. 8Band described in detail elsewhere herein, detectable signals from aplurality of such sites may be collected in a single waveguide 3101 (asensing waveguide). In a particular example, detectable signals (opticalradiation) from between 6 and 10 analyte sensing sites are collectedinto a single sensing waveguide and assayed. Detectable signals (opticalradiation) for each detectable signal (fluorophore) may be collectedover time, measured and plotted on an X-Y graph to obtain a slope basedon signal intensity vs time. As discussed in more detail below, theslope of the control graph may be compared with the slope of signalintensity vs time for a bodily sample such as handled as describedherein to calculate an amount of analyte present in the bodily sample.Although only one binding agent may be present, in other cases aplurality of different binding agents (antibodies) may be present in analiquot of a single reagent or in a single control metering well eachwith a different detectable label. In general, a separate control graphis generated for each detectable signal (for each antibody).

A method for analyzing a bodily fluid from a subject may also includethe step of passing the reacted sample from the subject over the atleast one analyte sensing site and conjugating reacted sample antibodyhaving the available epitope to first antigen in the at least onesensing site and thereby activating a first detectable sample signalfrom the at least one sensing site; after the passing the reacted samplestep, measuring over time detectable signal from the at least onesensing site to generate a second set of measurements; and comparing thesecond set of measurements to the first set of measurements to therebydetermine a level of first analyte in the bodily fluid; wherein firstreacted sample does not substantially bind to the first antigen in theat least one analyte sensing site if first analyte is bound thereto. Insome examples, a sample of bodily fluid is diluted prior to the mixingor incubating with a binding agent. A bodily fluid, especially an oralfluid such as saliva, may be relatively viscous and diluting the sampleprior to analysis may make it easier to handle and assay.

This may conclude the rapid test and the cartridge can be removed fromthe reader module. The disposable device 1000 may then be packaged in asealed container to be sent out to a forensic or other lab forconfirmatory testing. The sealed container may be a sealable bag such asa Ziplock bag or a standard evidence bag used by the law enforcementagencies, for example. In addition to using a standard evidence bag,chain of custody can be maintained and documented by use of barcodes orother identifiers which can be attached to the swabs and/or other partsof the system.

Assays as described herein may be especially useful for detecting asubstance of interest and especially for detecting a substance that mayalter cognition and affect a subject's actions or behavior (e.g., adrug, a drug of abuse, a legal substance, an illegal substance, ametabolite of such substances and so on). Substances of interest may bedetected directly or a form of a substance, such as a metabolite, may bedetected. In some examples, a single substance of interest may bedetected using the systems described herein and in other examples, aplurality of different substances may be detected using a multiplexassay. In some examples, a single substance of interest may be detectedusing two assays in a system, For example, or more control reagents maybe used to assay a single substance such as by using a first controlreagent to detect a first substance and using a second control reagentto detect a metabolite (or different epitope or different part) of thesame substance.

Substances that may be analyzed using the systems described hereininclude cannabinoids, depressants, hallucinogens, muscle relaxants,narcotics, sleep aids, and stimulants. Substances that may be analyzedusing the systems described herein include11-Hydroxy-Δ9-tetrahydrocannabinol (11-OH-THC, 11-hydroxy-THC, or11-nor-delta-9-THC-COOH), 11-nor-9-carboxy-THC (THC-COOH), amphetamine,another cannabinoid, a barbiturate, benzodiazepine, benzoylecgonine,buprenorphine, cocaine, d-Amphetamine (AMP), ecstasy (MDMA), ethylalcohol, fentanyl, heroin, heroin metabolite, hydrocodone, lysergic aciddiethylamide (LDS), mescaline, methadone, methadone metabolite,methaqualone, morphine, an opiate, oxazepam, oxycodone, phencyclidine,synthetic cannabinoid, tetrahydrocannabinol (THC cannabinoid), and soforth.

In some particular examples, one or more than one or all of thefollowing are sensed using the systems described herein: amphetamine,benzodiazepine, cocaine, marijuana, methamphetamine, and opiates. In aparticular example, at least three of benzodiazepine, cocaine, fentanyl,and marijuana (THC) are sensed.

Examples

Example 1 FIGS. 15A and 15B shows results of an assay signaldistribution as described herein for detecting marijuana (THC;tetrahydrocannabinol) in a sample. An assay is a balance betweenspecificity and sensitivity: calling true negatives (TN; calling aresult that was actually negative negative), false negatives (FN;calling a result negative when it was actually positive), falsepositives (FP; calling a result positive when it was actually negative)and true positives (calling a results positive when it was actuallypositive). FIG. 15A shows a graph of probability for (from L to R) truepositives, false positives, false negatives, and true negatives usingthe systems and assays described herein. A threshold value of about 0.7×provides a balance between minimizing both false negatives and falsepositives (see the point at which these two curves overlap) andmaximizing true negatives and true positives. Other threshold valuescould also or instead be chosen to increase/improve either specificityor sensitivity. FIG. 15B shows a graph of error rate vs signalthreshold. At a threshold around 0.7 (0.72) the error rate from falsepositives (the curve starting high on the left side of the graft) andthe error rate from false negatives (the curve starting low on the leftside of the graft) are both less than 6%. This graph assumes that the 30measurement of the samples are normally distributed.

Example 2 is shown in FIGS. 16A and 16B. These figures show an exampleof error rate results from a multiplex assay as described herein fordetecting cocaine (COC), marijuana (THC; tetrahydrocannabinol) andbenzodiazepine (BZO). FIG. 16A shows error rates for false positives(the bars on the left side of the graph; left of 0%)) and falsenegatives (the bars on the right side of the graph; right of 0%). Errorrates are less than 10% for the analytes tested cocaine (COC), marijuana(THC; tetrahydrocannabinol) and benzodiazepine (BZO). False positive andfalse negative error rates for cocaine are around or less than 4% and 6%respectively for cocaine; around or less than 6% and 4% respectively forTHC, and around or less than 2% and 2% respectively for benzodiazepine(BZO) at 0.6×. Other threshold values could be chosen to minimize eitherfalse positives or false negatives.

Example 3 is shown in FIGS. 17A-17C. These figures show results from amultiplex assay using the systems and methods described herein includingdried beads containing reagents and a serpentine mixer for detectingcocaine (COC-M), fentanyl (FEN), morphine (MOR) and benzodiazepine(BZO-O). Errors are less than 10% and less than 4% in an FIG. 17A showserror rates for false positives (the bars on the left side of the graph;left of 0%) and false negatives (the bars on the right side of the graphright of 0%). Error rates are less than 10% for the analytes tested.False positive and false negative error rates for morphine are around orless than 1% and 0%, around or less than 0% and 0% respectively forcocaine, and around or less than 1% and 0% respectively for fentanyl,and around or less than 4% and 4% for benzodiazepine (BZO-O), with falsepositives at 0.5× and false negatives at 1.5×. Other threshold valuescould be chosen to minimize either false positives or false negatives.FIG. 17B shows assay signal distribution for the fentanyl (FEN) assayshown in FIG. 17A for fentanyl at 0.5× and 1.5×. FIG. 17C shows a graphof the probability (Y-axis) of an assay signal distribution for thebenzodiazepine (BZO-O) for the assay shown in FIG. 17A.

FIGS. 19A-19B show (with individual illustrations) one example of amethod of operation of an apparatus as described herein for samplingsaliva. In this example, the cartridge, including a saliva collectionsystem (also referred to as a saliva collection sub-systems) is removedfrom a sterile packaging 1901, and includes the cartridge body (coupledto the collection body) and a cap. The first and second swab pistonsextending from the collection body may then be inserted into a subject'smouth to collect saliva 1903; an indicator (colorimetric indicator) onthe side of the device may change color to indicate when it is full, andsaliva collection is complete 1905. The cap may then be inserted andsnapped over the first and second swab pistons (containing the salivasample); the action of attaching the cap may pierce a frangible coverwithin the cap and may force the one or more fluids (e.g., a dilutionfluid in one side, corresponding to the first swab piston, and apreservation solution in the second side corresponding to the secondswab piston) to mix with the saliva samples. The first and second sidesmay be isolated from each other (fluidically isolated) 1907. The sampleto be immediately tested is diluted a predetermined amount and dispensedinto the diluted sample cavity within the cartridge. The cartridge maythen be inserted into a reader 1909 for processing and reading.

FIG. 19B continues the method shown in FIG. 19A. In FIG. 19B, thecartridge reader may then process the fluid within the cartridge via thefluidic circuit(s), as will be described in greater detail in referenceto FIGS. 20A-20N, below, and resulting signals may be read out, asdescribed above 1911. The readout may be qualitative (e.g., above athreshold, within a range indicating “positive”, “negative” or“inconclusive”, etc. for the presence/absence of a drug of addiction),and/or it may be quantitative (estimating concentration values). Theoutput may be presented and/or stored and/or transmitted.

The entire cartridge may then be stored and/or transmitted forconfirmation processing, e.g., at a remote laboratory 1913, 1915. Forexample, the cartridge may be sealed in a package. The second sample(mixed with the preservation solution within the cartridge, e.g., thecollection sub-system portion of the cartridge) may be kept indefinitelyuntil confirmation testing is desired. When retesting of the storedsample is desired, the cartridge may be unsealed, e.g., the tab on thecollection device may be broken, and the confirmation test performed1917.

Any of the processing steps described herein using the microfluidics onthe cartridge may include manipulation, e.g., by a reader, of thefluidics circuit within the cartridge. FIGS. 20A-20N illustrate oneexample of fluidics circuit (similar to that shown in FIG. 7). In FIG.20A, the circuit is illustrated; FIG. 20B shows a legend or key that maybe helpful when reviewing the exemplary operation described and shownschematically in FIGS. 20C-20N.

FIG. 20C illustrates the initialization step, in which the pump(diaphragm) may be set up so that both pushing and pulling of fluidthrough the device may be allowed. In FIG. 20C, the reader (e.g., a pumppiston on the reader) may be pushed at least partway in to deflect(e.g., approximately 50%) the pump diaphragm in the cartridge, as shown.In this case, valves in the reader keep the vents on either side of thediluted sample cavity closed, but leave the waste vent (downstream ofthe waste reservoir) open, so that only air may pass into the channels.The swab piston (also referred to herein as a swab plunger) in thesaliva collection portion has already pushed diluted sample into theDiluted Sample Cavity (DSC) in the cartridge. A cap stop may preventcapillary movement of the sample.

In FIG. 20D, the sample may be metered (e.g., a predetermined volume ofdiluted sample) by the circuit. Once the reader has closed the wastevent valve and opened the vent downstream of the diluted sample cavity,the reader may then controllably release the pump piston so that thepump (diaphragm) applies negative pressure to pull a sample into thesample metering well (SMW) until a fluid sensor detects a fluid meniscusand stops the pull by holding the pump piston in place. The sample maybe ‘cleaved’ (e.g., so that a bolus of air is added to cut off themetered sample from the diluted sample cavity), by the reader closingthe vent downstream from the diluted sample cavity and opening the ventbetween the diluted sample cavity and the metering well (“sample well”).The pump may be allowed to pull fluid slightly, drawing a bolus of airbehind the metered sample in the sample well, as shown in FIG. 20E,accurately separate a slug of metered volume of sample.

In this example, a lyophilised bead (e.g., including a fluorescentlylabeled antibody to the drug(s) to be identified) may be present in thesample well and may dissolve in the sample. The fluid may then be pulledinto the serpentine mixer and moved back and forth within the mixermultiple times to achieve thorough mixing. This is illustrated in FIG.20F. The reader may achieve this by extending and retracting the pumppiston to controllably push and release the pump diaphragm on thecartridge, resulting in pushing and pulling the sample fluid within themixer; as illustrated above, the mixer may be a serpentine channel. Oncemixed, the fluid may be left in the sample channel and allowed toincubate, as shown in FIG. 20G. In some variations, the pump may bereleased (e.g., allowed to fully relax to a neutral position), byopening the vent downstream from the waste channel, and closing thevents upstream and downstream from the diluted sample cavity.

The control solution within the blister pack may then be dispensed. Forexample, in FIG. 20H, the blister pack is burst by applying a force(e.g., from a piston) to push the blister pack against the needle withinthe cartridge, and the control fluid is pushed into the control meteringwell (CMW) till a fluid sensor detects the meniscus and stops the reader(e.g., a piston for pushing the blister pack) from pushing further. InFIG. 20I, the control fluid may be metered by the reader pushing on the(now air-filled) pump diaphragm. The pump then pushes air into thecontrol channel to accurately separate a slug of metered volume ofcontrol fluid. In this example, a lyophilised bead (e.g., fluorescentlylabeled antibody) in the CMW (control metering well) may dissolve in thecontrol fluid. As shown in FIG. 20J, the control solution (fluid) maythen be pulled into the serpentine mixer and moved back and forth withinthe mixer multiple times to achieve thorough mixing, again by applyingpushing force (or relaxing the pushing force) to allow the diaphragm tomove in and out, pushing and pulling the control solution through thesecond serpentine mixing channel. The control fluid is then left in thecontrol channel to allow incubation. After incubation, the control fluidis pushed into the chip channel and data acquisition is done, as shownin FIG. 20K. In this example, the solution may be passed onto the chipand evanescent signals detected as described above. Thereafter, thecontrol fluid may be pushed into the waste well till the chip channel isempty, as shown in FIG. 20L, by the reader pushing (via the pump piston)on the pump diaphragm.

Next, the sample may be pulled into the chip channel and dataacquisition done, as shown in FIG. 20M. The vent downstream to the wastechannel is closed, and the vent between the sample (metering) well andthe diluted sample cavity may be opened, as shown, so that releasing thepump piston by the reader allows the pump diaphragm to apply negativepressure to pull the metered sample solution over the chip, allowingevanescent reading by the chip. Finally, the sample may be pulled intothe control channel and pump chamber, as shown in FIG. 20N.

In general, any appropriate reader may be used. A schematic of oneexample of a desktop reader is shown in FIGS. 21A and 21B. In thisexample, the reader may include one or more processors (controllers)including a memory, and control circuitry, for controlling the pumppiston, the valves, the fluid sensors, and the optical illuminationsource and optical detector for reading from the photonics chip, as wellas hardware, software and/or firmware for processing signals from thephotonics chip. The reader may also include one or more outputs(displays, memory, wireless or wired transmitters, printers, removablememory, etc.

In general, the reader apparatuses described herein (e.g., the opticalreader devices) may include a cartridge holder for holding any of theremovable cartridges described herein, a scan head coupled to a laserlight source and an optical detector for applying excitation light tothe photonics chip of a cartridge in the holder and detecting an emittedsignal, a microfluidics manipulator for manipulating fluids in thecartridge (e.g., one or more valve controls, one or more membrane pumps,and one or more optical fluid sensors), an output for outputting thereadings, and a controller for controlling and coordinating theoperation of the scan head, light (e.g., laser) source(s), opticaldetector(s), microfluidic manipulator(s) and output. The apparatus mayalso include one or more inputs. The controller may include controlcircuitry (e.g., one or more processors, memory accessible to the one ormore processors, clocks, wireless communications circuitry, etc.).

For example, FIG. 21C is a schematic of one example of an apparatus asdescribed herein. In this example, the reader 2100 includes a cartridgeholder 2151, which may be referred to herein as a clamp, which may holdand secure the cartridge within the reader and align it. The cartridgeholder may include a variety of alignment surfaces (e.g., pins,registration surfaces, etc.) as described in greater detail below. Thecartridge holder may include or may be coupled with one or more valvescontrolled by one or more valve controls 2161. The valves may be plunger(e.g., solenoid) and/or pinch valves that may interface the valveopenings on the cartridge to regulate fluid flow, as described above.One or more force applicators (e.g., membrane pump actuator 2163) may beincluded as well, to push against the membrane pump in the cartridge.The force applicator may be a piston, rod, or otherextendable/retractable member that may apply force against the pumpmembrane by moving towards or away from the membrane. In some variationsthe force activator is a geared member (e.g., rod) that is controlled tomove forward or backwards to deflect or relax deflection of the pumpmembrane, as described above. In some variations, the force applicatormay be a balloon that is inflated/deflated to deflect or relaxdeflection. In general, the membrane pump actuator 2163 may apply forceto increase deflection of the pump membrane of the cartridge, to hold adeflection of the pump membrane, and/or to relax deflection of the pumpmembrane. The membrane pump actuator may be integrated with thecartridge holder and/or it may be separate from the cartridge holder. Insome variations the membrane pump actuator includes an arm for applyingforce to the membrane and a driver (e.g., a mechanical drive, apneumatic driver, an electromagnetic driver, etc.) for driving the armagainst the membrane. In some variations the arm may include a roundedend (e.g., a ball-shaped end, etc.) to avoid damaging the membrane pump.The arm may be hinged. A mechanical driver may include one or moregears. The driver may also include a sensor or detector for detectingthe position of the arm relative to the cartridge and/or membrane pump,and/or for detecting the force applied by the driver. The detectedposition and/or force may be used as feedback to regulate the pumping.

The apparatus may also include a second force applicator for applyingforce to puncture, rupture or otherwise open the blister pack. Forexample, the apparatus may include a force applicator (e.g., rod,striker, etc.) for applying force to drive a piercing element (e.g., inor on the cartridge) to open a blister pack. The membrane pump actuatorand blister pack force actuator may be controlled by the controller2150.

One or more non-contact, optical fluid sensors 2165 may be included aspart of the cartridge holder and/or in communication with the cartridgeholder. As mentioned above, fluid sensors 2165 may be non-contactoptical reflectance or transmission type sensors. The fluid sensors maycommunicate with the controller 2150.

The reader 2100 may also include a scan head 2159 within the readerhousing. In general, the position of the cartridge in the cartridgeholder is adjustable relative to the position of the scan head.Typically the scan head 2159 is movable relative to the cartridgeholder, however in some variations the cartridge holder may also beadjustable or the scan head may be fixed in position while the cartridgeholder position is adjusted. In FIG. 21C, the scan head position ismovable relative to the cartridge holder and a scan head actuator mayadjust the position of the scan head relative to a cartridge within thecartridge holder. The scan head actuator may be configured to move thescan head to adjust one or more of the x, y or z position of the scanhead (and thus the output of the light/laser source 2155 and the inputfor the optical detector 2157) so that the scan head may optimallycouple with the photonics chip, e.g., the edge of the photonics chip ofthe cartridge having access to the excitation waveguides and emissionwave guides in the chip (see, e.g., FIGS. 8A-8B). In some variations thepitch, yaw and/or roll of the scan head may also be adjusted.

The light source 2155 may be part of the scan head or it may be separatefrom the scan head. In some variations the light source is a pluralityof laser diodes that each couple to the scan head through a fiber line(e.g., as described below, a polarization maintaining single modefiber). The optical detector(s) 2157 may be part of the scan head or maybe separate from the scan head. In some variations the optical detectorsmay be detectors (e.g., photodiode detectors) that couple via a fiber tothe scan head. For example, an array of photodiode detectors may coupleto the scan head via a multimode fiber. The scan head may include afiber coupler, and an end of each of the emission fibers (e.g.,polarization maintaining single mode fibers connected to the laserdiodes) and an end of each of the sensing fibers (e.g., the multimodefibers each coupled to a photodiode) may be exposed in a configurationthat is complimentary to the configuration of the emission and detectionwaveguides on the edge of the photonics chip, as shown in FIGS. 8A-8Band 9A.

The controller may also control operation of the scan head actuator toalign the scan head (and thus the excitation source, e.g., laser source,and the optical detector) with the cartridge, and may coordinate theapplication of control fluid and then test sample into the wells of thephotonics chip and detection of signal from control and sample.Typically the reader and cartridges described herein may detect bothcontrol and sample signals from the same wells, thus minimizing error.

The controller may also receive input from a user via one or more inputs2171, which may be a keyboard, touchscreen, dial, control, buttons,and/or wireless input from a remote processor (e.g., smartphone,computer, laptop, tablet, etc.). The controller may provide output 2169to one or more screens (e.g., touchscreen, display, etc.), files,memory, printers, etc.

FIGS. 21D-21N illustrate another example of a reader device. In thisexample, a cartridge 2144 is shown inserted into the reader device 2100.The reader device in this example includes a scan head assembly 2144,including a first collection of fibers 2148 that connect to a pluralityof light sources (e.g., laser diodes, not shown) via a connector 2152. Asecond plurality of fibers 2154 connects on one end to the scan head andcouples to a plurality of detectors (e.g., photodetectors, not shown) todetect evanescent signals from the chip. The second plurality of fiberscoupled to the detectors through a connector 2156. The fibers may beheld in a channel 2165. The scan head assembly may be moved relative tothe cartridge holder by one or more actuators (e.g., linear actuators)2153.

The reader device in FIG. 21D also include a holder (clamp) assemblyforming a slot 2158 into which the cartridge his inserted. The slotincludes a reference surface in the z-direction (a pin at the back ofthe slot, not visible in FIG. 21D), as well as a reference surface inthe x-direction (e.g. along the long side of the slot). The slot mayinclude a track, flange, lip, rim, etc. for guiding and securing thecartridge (e.g., by mating with a corresponding lip, ring, flange. pin,etc.) on the cartridge. The cartridge holder (cartridge holder assembly)may include a top 2162, which in this example forms the opening andupper and side walls, and a bottom of base plate 2164, which is visiblein FIG. 21E, showing the same device as in FIG. 21D, without a cartridgeinserted.

This device may also include a plurality of valves 2161 and a membranepump actuator 2163. In the example shown in FIG. 21D, the pump actuatoris a rocker arm that is driven by a linear actuator 2174. The linearactuator may push or pull one end of the rocker arm and may lock therocker arm in a pushed or pulled position, controlling the deflection orrelaxation of a membrane pump of a cartridge held in the cartridgeholder. As described below, the end of the rocker arm contacting themembrane pump may be ball-shaped (not visible in FIG. 21D or 21E). Asecond actuator 2188, also shown configured as a rocker arm that isconnected to a linear actuator 2190 and may be used to apply force torupture or otherwise open a fluid container (e.g., blister pack) on thecartridge.

The reader device may also include a controller having one or moreprocessors (not shown) and one or more memories. In any of thesevariations, the components shown in FIGS. 21D and 21E may be covered bya housing, which may have an opening, door, etc. for inserting thecartridge (see, e.g., FIGS. 21A-21B).

FIG. 21F shows a back perspective view of the device of FIGS. 21D-21E.The cartridge holder, actuators and imaging sub-systems may be supportedon a frame 2149.

FIG. 21G shows a side view of the device of FIGS. 21D-21F, showing thegap 2192 between the imaging sub-assembly 2196 (including the scan head,fibers, light source, detectors), and the holder sub-assembly 2198 (andtherefore a cartridge and photonics chip held by the cartridge holder).As described above, the controller may move the scan head to align thefiber ends on the scan head for emitting and receiving light from thechip with the waveguides on the chip.

FIGS. 21H and 21I show back and front views, respectively, of the samedevice shown in FIGS. 21D-21G. FIGS. 21J and 21K show top and bottomviews, respectively. FIG. 21L shows another example of a sideperspective view of the device of FIGS. 21D-21K, showing the gap 2192between the scan head and the cartridge chip when the cartridge is heldby the cartridge holder. FIGS. 21M and 21N show an enlarged view of thegap; in FIG. 21N the outer portions of the scan head (e.g., an upperscan head mount 2134 and a lower scan head mount 2136, present in FIG.21M) removed to show the ends of the fibers 2138 held on the gap-facingside of the scan head.

Optical Path Polarization

Any of the reader apparatuses (e.g., optical readers) described hereinmay be configured to control the polarization of the light for signaldetection to a cartridge's photonics chip and/or received from photonicschip.

First generation hardware of the reader did not utilize any polarizationmaintaining hardware. This lead to high variability of opticalcharacteristics from one apparatus to another. After ruling outmechanical variances as the root cause of the machine to machinevariability, EM simulations were performed for the photonic chiparchitecture of our system. See FIG. 1.

FIG. 22 is a graph showing field mode profiles for an optical reader(such as the optical readers discussed and illustrated above) in whichboth transverse-electric (TE) polarization (also referred to as Spolarization) and transverse-magnetic (TM) polarization (also referredto a P polarization) are compared. In FIG. 22, the electric field modeprofiles of the two orthogonal modes of the waveguide are quitedifferent, e.g., the input coupling efficiency is different. Thecoupling efficiency to each of the two modes is given by the modeoverlap integral with the input Gaussian beam from the scan head fiber.FIG. 23 shows a TM mode coupling that is significantly greater than theTE mode coupling efficiency in the tested optical reader apparatus. Thisdemonstrates a large variation in reader optical characteristics ifcoupled into TE mode vs TM mode, as this would result in differentamounts of light into the system for a given laser output.

In addition to the significant difference of input coupling efficiency,there is also a large difference at the well interfaces of the couplingto fluorophore, e.g., in the photonic chip(s) of the cartridge(s) beingread by the optical reader. The fluorophore absorbed energy isproportional to the square of the electric field at that point in space.FIGS. 24 and 25 show the electric field profiles for the two orthogonalTE and TM modes in various configurations of the waveguide (e.g., a fourlayer waveguide configuration and a three-layer waveguideconfiguration). In any of the tested configurations, at the well surfacewhere the fluorophore will sit (≈100 nm), the TM mode has a large spike2501 and its magnitude is significantly larger than the value 2401 atthe surface for the TE mode.

An optical experiment was used to experimentally test these simulationresults. Using free space optics, the linear polarization state of lightthat is outputted from the scan head was controlled. Using a fixed laserpower, an optical jump experiment was performed with the opticalpolarization being TE and also TM. As shown in FIG. 26A, TM polarizationhad a factor of 2.5× better signal compared to the TE mode for the samelaser power.

The simulation and experimental results such as those described above,illustrate the surprising polarization sensitivity of the optical readersystem(s) and cartridge(s), e.g. photonic chips. In particular, theconfiguration of the optical readers and cartridge chips describedherein respond surprisingly well to the use of TM (e.g., S) polarizedlight for both excitation and detection. Thus, in any of the apparatusesdescribed herein, the optical path may be configured to maintain a knownpolarization (e.g., TM polarization) throughout. This may be done by theuse of polarization-maintaining fibers pigtailed onto diode lasers andalso using polarization-maintaining fibers in the newly designed scanhead in general. The polarization axis of our optical system may beconfigured to optimally interface with the photonic chip using the TMmode.

FIG. 26B illustrates one example of an optical reader apparatus 2600including a scan head 2601, a scan head actuator 2617, a controller 2619and a cartridge holder 2615. The scan head may be aligned with acartridge (e.g., the edge of a photonics chip in the cartridge) both topermit the one (or in some cases a plurality of parallel) excitationbeam(s) that are emitted by the scan head to be properly centered on theedge region of the chip so that light may pass into the chip to enterinto the one or more waveguides of the chip. As described herein, whenthe photonics chip includes a plurality of parallel waveguides that arearranged in an array in which excitation row are crossed by detectionrows (see, e.g., FIGS. 8A and 8B), so that evanescent transmission maybe detected in the detection row(s), the polarization of the light maybe critical and should be controlled as described herein. Thus, any ofthese apparatuses may be configured to control the polarization of thelight applied and received by the apparatus, and particularly so thatthe apparatus may emit and in some variations receive, TM polarization.

For example, in FIG. 25B, the laser light source 2603, transmissionfibers 2605 and scan head 2601 may form a polarization axis 2609 that isconfigured to maintain the TM polarization of light transmitted by thesystem so as to optimally match the polarization of a photonics chip(e.g., including an array of intersecting waveguides) that permitevanescent light transmission. In some variations the scan head mayinclude a laser light source 2603 to which a plurality ofpolarization-maintaining fibers 2605 are connected. Alternatively, asshown in FIG. 26C, the laser source (e.g., LEDs) may be separate fromthe scan head and may be coupled to the scan head through thepolarization maintaining fibers. Both the laser source and thepolarization maintaining fibers may be configured so that they arematched in polarity (e.g. TM polarization) with the photonic chip. Thescan head may also include or be connected to the optical detector 2607via a plurality of multimodal fibers 2525. In some variations the scanhead includes an interface 2613 that holds the ends of the fibers (e.g.,the polarization maintaining fibers and/or the multimodal fibers) in anarrangement that matches the arrangement of the waveguides (the emissionand excitation waveguides) in the photonics chip. The opticaldetector(s) (e.g., photodiode detector(s)) may be arranged as an arrayof sensors that detect signal(s) from the photonics chip when properlyaligned, concurrent with excitation. In some variations, any portion ofthe scan head may include a polarizer (e.g., a TM polarizer) to removeor redirect TE polarized light so that the scan head may be positionedby moving the scan hear relative to the interface edge of a chip (orchips) on a cartridge held in a cartridge reader. For example, in somevariations a polarizer may be between the optical sensor and/or thecartridge once it is loaded in to the cartridge structure. Alternativelyor additionally, a polarizer (e.g., TM polarizer) may be positioned infront of the optical sensor(s), e.g., between the optical sensor(s) andthe fibers 2605; and/or between the laser source and the plurality offibers.

The scan head may also include one or more lenses, filters, and/or otheroptical elements. For example, each optical fiber end may terminate in alens or lensing element. The ends of the fibers may be arranged in apattern configured to match the pattern of emission and detectionwaveguides ends in the photonic chip edge. For example, the opticalfiber ends may be arranged in a line, and individual fiber ends (and/orgroups of fibers, such as emission and detection fibers) may beseparated by the same distances as the waveguides in the chip (see,e.g., FIGS. 8A-8B).

In some variations, the apparatus may be configured to adjust thepolarization of the system before or during the assessment of analytesignals. For example, the controller 2619 of the apparatus may beconfigured to adjust the position of all of the scan head or a portionof the scan head (e.g., the interface 2613, also referred to as acartridge interface) relative to the edge of the chip in the cartridgeholder 2615. The position may be adjusted in x, y, z and/or angle (e.g.,pitch, yaw, and/or roll) relative to the cartridge holder.

FIG. 26C shows another example of a schematic of a portion of an opticalreader apparatus for detecting evanescent signals from a photonic chip2680. In FIG. 26C, the optical reader apparatus includes a scan head2681 that may be moved within the optical reader relative to thephotonic chip in order to pair with the excitation-receiving waveguides(e.g., four excitation receiving waveguides such as those shown in FIGS.8A-8B). The photonic chip is oriented so that the waveguides for bothexcitation and detection have ends that are arranged along an edge ofthe chip, and this configuration of waveguides has an optimalpolarization that is TM polarized. The polarization of the chip ismatched by the polarization of both the light source (e.g., laser diodes2699) and the light path from the laser diodes to the photonics chip(including a plurality of polarization-maintaining single mode fibers2691, 2685 and fiber coupler(s) 2687′. Each excitation waveguide maymatch with a TM polarized light path extending from an individual diodelaser (e.g., a 635 nm fiber pigtailed diode laser) and may couple via apolarization maintaining single mode fiber and fiber coupler to the scanhead. The return (sensing) path may include a plurality of photodiodedetectors 2697 that couple to the scan head via a plurality of multimodefibers 2683, 2689 and fiber couplers 2689. Each emission/sensingwaveguide may couple to an individual photodiode detector.

In some variations the angle of polarization may be matched within +/−afew degrees (e.g., 30 degrees, 25 degrees, 20 degrees, 15 degrees, 10degrees 5 degrees, 2 degrees, 1 degree, etc.).

Precision Alignment of the Cartridge

Any of the apparatuses described herein may also or alternatively beconfigured to control the precise alignment between the cartridge and ascan head. In particular, a cartridge holder may be configured tosecurely but releasably and repeatably holding a cartridge so that theedge of the photonics chip, on which a detection reaction (such as thosedescribed above) may be sensed. Alignment may be particularly importantbetween the scan head and a cartridge held within the reader. Althoughthe reader should allow some tolerance when inserting a cartridge, sothat the cartridge may be easily inserted and reliably read, thedistance and orientation between the scan head and the photonic chip maybe precisely controlled to allow rapid and accurate reading of thecartridge. In addition, the actuation of the fluidics in the cartridge(e.g., valves and membrane pump) may be aligned in order to allow thedevice to be operated reliably. Described herein are methods andapparatuses for coupling a cartridge having fluidic components (e.g.,valves, membrane pump, etc.) and one or more photonic chips so thatthese components of the cartridge are aligned with the correspondingcomponents of the reader.

FIGS. 27-42 illustrate examples of optical readers that include acartridge holder (clamp) that is configured to hold the cartridgesecurely and precisely aligned with the scan head. In general, theapparatuses described herein may be configured to automatically adjustthe alignment between the scan head and the cartridge, particularly anedge of one or more photonics chip of the cartridge. Thus, describedherein are methods and apparatuses for holding a sample-collectingcartridge that include a clamp that is particularly configured to permitrobust use, so that even after repeated use with different cartridges,subsequent use may still result in precise positioning and alignmentbetween the scan head and the cartridge.

The cartridge may be inserted into the optical reader by inserting intoa cartridge interface 2105 (e.g., an opening, lid, tray slot, etc.) inthe reader. Once the cartridge is inserted into the cartridge interfaceit may be clamped into position. Clamping may be automatic or manual. Insome variations the apparatus detects insertion of a cartridge andclamps onto the cartridge. Thus, the cartridge interface may open into acartridge holder that may include a clamping interface (e.g., an openingan open clamp). In some variations, the apparatus includes a clamphousing (e.g., the cartridge holder includes a clamp housing) that hasone or more slots cut into the side of the clamp housing; the cartridgemay have wings or other mating features (pins, rails, etc.) that matewith the slots. See, e.g., FIG. 27, showing one example of an end regionof a cartridge including at least one wing 2705 and a cut-out region fora wing 2709 on the cartridge. When engaging with the optical reader, acartridge such as the one shown in FIG. 27 may be pushed forward(showing as the Z-axis, corresponding to a long axis of the cartridge inthis example) until a reference surface 2711 on or near the front of thecartridge (e.g., the reference surface in the x axis 2711 and/or thereference surface in the y axis 2713) hits a cylindrical surface of areference pin in the reader and stops.

The device may also include an output (e.g., display, screen, etc.,including a touchscreen) 2169 and/or an input (e.g., in FIG. 21A-21B, atouchscreen).

In some variations, the clamp securing the cartridge includes a ballplunger on one side of the clamp housing which pushes against one of thewings (in the X-axis) that extend from the side of the cartridge. Thiswing has a cut out at a certain location such that when the cartridge isall the way in the clamp the ball plunger pushes the cartridge wall upagainst two reference surfaces (e.g., against the Z-Axis and X-Axis).The reference surface in the Z-axis may be a pin that is part of theclamp housing. Another reference surface may be the wall of the topclamp housing opposite the ball plunger. The ball plunger may keep aconstant force on the cartridge while it is fully inserted. While thecartridge is fully inserted, the clamp base can be raised (Y-axis) whichforces the cartridge up against the third reference surface (e.g., theunderside of the top of the clamp.) and may hold the cartridge preciselyand securely in place during usage.

As discussed above, there may be an optical chip in the cartridge whichis optically scanned. The location of the front surface of this chip maybe precisely placed in the X-Y-Z-axis. The back of the chip in theZ-Axis may be placed in contact with a reference wall in the top frontof the cartridge.

In any of these variations, the cartridge holder (e.g., the clamp base)is temperature controlled. Temperature control may allow the cartridgeto be maintained at a constant temperature and/or may allow thecartridge temperature (all or a local region of the cartridge) to beadjusted. For example, FIG. 39 illustrates one example of a cartridgeholder portion of a reader apparatus that is configured to control thetemperature. In FIG. 39, the temperature may be sensed (e.g., the tempof the cartridge) by included two or more temperature sensors 3905 onthe cartridge holder in regions facing or in contact with the cartridge.In some variations the cartridge holder may also include one or moreheaters 3908. The cartridge and/or the reader may include one or moreinsulating regions (e.g., thermally insulated regions), For example, inFIG. 39, the cartridge holder includes a partition 3913 (e.g., amaterial cut or region to help confine heat from another region of thecartridge (e.g., thermally isolating the front part of the clamp(cartridge holder).

The cartridge holder (e.g., the clamp mechanism) may be mechanicallyand/or electrically and/or pneumatically controlled. For example, thecontroller in the optical reader may coordinate the operation of thecartridge holder, including one or more of: sensing the cartridge withinthe cartridge holder, closing/opening the clamp of the cartridge holder,coordinating the application of force in the x, y, and/or z direction toretain and align the cartridge, etc. For example, in some variations thecartridge and the optical reader (e.g., the cartridge holder) may beconfigured for pneumatic and fluidic operations.

In addition to holding the cartridge in a predetermined manner, foralignment with the optics of the optical reader, the reader, includingthe cartridge holder, may be aligned so that the controller maycoordinate the movement of fluid (microfluidics) within the cartridge,as discussed above. For example, in FIG. 27, a cartridge may include apump membrane 2715 that may be operated by a pump membrane actuator(e.g., a piston or other member) in the reader to apply positive and/ornegative force (e.g., by pushing, holding, or releasing the membrane)within the cartridge. The cartridge may also include one or moreblisters 2717 including a fluid, as described above. The controller ofthe optical reader may further coordinate the release of fluid from theblister. A chip (e.g., photonic chip) 2721 is typically exposed at oneend. In FIG. 27, the exposed edge of the chip is located in the middleof the x-axis face about midway through the y-axis face.

FIG. 28 shows one example of a partial section through a cartridgeholder 2800 including a clamping portion. In this example, the cartridgeholder includes a cut out slot region 2803, 2803′ on either side forengaging wings on the cartridge (extending into the reader from theopening in the reader in the z-axis direction, as shown in FIG. 27). Theopening formed for the cartridge in the cartridge holder may alsoinclude at least one reference pin 2805 in the z-axis. A referencesurface in the y-axis 2807 as well as a reference surface in the x-axis2809 may assist in alignment in these directions. By choosing andconfiguring the reference surfaces in the clamp and cartridge, the stackup of tolerances may be minimized. In addition, the ball plunger andmovable clamp base 2831 may provide precise and repeatable positioningof the cartridge. FIG. 28 also shows some of the regulator members 2811(e.g., valve controls) that may open/close air vents in the cartridge tocontrol fluid movement (as described above). Additional regulators(e.g., mechanical regulators, such as pistons, etc.) may be used toapply force to regions of the cartridge to move fluid through thecartridge (e.g., pushing on the membrane(s)).

FIG. 29 illustrates an example of a cartridge showing it clamped ontoone example of a cartridge 2922. In FIG. 29, the X and Y referencesurfaces 2907, 2909 are shown making contact with the correspondingsurfaces on the cartridge. The cartridge holder includes a clamp top2911 that secures the cartridge 2922; wings on the right side 2913 andleft side 2915 of the cartridge may engage with slots in the cartridgeholder, as shown. The wings may guide the cartridge into the clamp butare not necessary as an alignment feature; by themselves, the wings maynot secure the cartridge in position adequately, because they mustinclude tolerance for inserting, removing and sliding the cartridgein/out of the apparatus.

In general, the clamp (e.g., cartridge holder 3000) may include one ormore alignment pins, such as one or more ball plungers, that are keyedto provide a force in a predetermined direction to secure the cartridgein the cartridge holder of the reader. For example, FIG. 30 illustratean example of a ball plunger 3005 that engages with the cartridge 3001.The ball plunger is biased to extend in the x direction; inserting thecartridge into the cartridge holder initially pushes the ball plungerback. As shown in FIG. 30, the ball plunger 3005 (an x- and z-directedball plunger) may rest on a corner 3003 of the cartridge when thecartridge is fully inserted. The force from the ball plunger is directedin the x and z directions (though the ball plunger moved in the xdirection primarily). In this example, the ball plunger engages with ashoulder region of the cartridge about midway along the z-axis of thecartridge.

FIG. 31 is similar to FIG. 30, in which the cartridge holder has beenmade transparent, showing just the ball plunger 3105 portion of thecartridge holder, as well as a portion of a cartridge 3100. As in FIG.30, the ball plunger rests on a corner 3103 of the cartridge (shoulderregion) when the cartridge. As the cartridge is inserted into thecartridge holder, the ball plunger pushes against a side surface 3107 ofthe cartridge, which forces the cartridge against the reference wall(e.g., the y reference surface).

Similarly, as shown in FIG. 32, the cartridge 3200 (top half of acartridge is shown in FIG. 32) may include a shoulder region (part of acut out portion on the lateral side of the cartridge) that the ballplunger 3205 may engage with. The cartridge may also include one or morereference pins 3207 and/or walls.

As mentioned, any of these apparatuses may include one or more actuators(e.g., mechanical actuators, valve actuators, etc.) for processing thesample, including the valve actuators 3305 and one or more mechanicalactuators for applying force to the cartridge, e.g., a membrane on thecartridge, to move fluid. The mechanical actuator may be a piston or, asshown in FIG. 33, a rocker arm 3301, 3301′ that is motor controlled. InFIG. 33, the rocker arms may be independently controlled to assist inprecise metering and movement of the fluid in the cartridge. In FIG. 33,an optical sensor 3307 may detect when the cartridge is inserted intothe holder, as well as one or more additional sensor components, such asa flange 3309 for home positioning sensors (e.g., detecting the positionof the cartridge holder and/or cartridge. In some variations the sensor3307 and/or additional sensors may detect fluid within the cartridgeheld in the cartridge holder.

For example, a reader, including the cartridge holder portion of thereader, may include additional sensors for monitoring processes withinthe cartridge, in addition to monitoring the position of the cartridge.For example, FIG. 34 shows an example of a pair of optical sensors 3403for monitoring fluid within the cartridge, including (as discussedabove) the presence of fluid in the mixing channel, etc. FIG. 34 alsoshows detail of the seals (e.g., O-rings) that may be included as partof the cartridge holder portion of the reader (alternatively in somevariations, they may be part of the cartridge, or of both the cartridgeand the reader). The O-Rings provide an air tight seal between thecartridge and the clamp base.

FIG. 35 shows an overhead view of the optical sensors for fluidmonitoring similar to the side view shown in FIG. 34. Thus, in thisexample, four fluid sensors 3505 are included.

FIG. 36 shows another view of a cartridge holder portion of a readerapparatus, without a cartridge inserted into it. In FIG. 36, the ballplunger 3603 shown on one side of cartridge-holding portion, and a pairof mechanical regulators, showing as rocking arms that include a toolingball 3605 at the end of the rocking arm, to apply force to thecartridge, such as a pump membrane, in order to drive fluid through thecartridge. In this example, the tooling ball provides a sphericalcontact surface between itself and a pump membrane (e.g., pumpdiaphragm) or a blister pack. The spherical shape may provide a constantcontact shape throughout the slight arc of the tooling ball's path. Thecontact surface area may change throughout the travel because the ballmay go deeper into the blister pack and/or pump membrane.

In some variations the pistons of the valves may be actuated by a linearactuator 3705, as shown in FIG. 37. In this example the valves 3709 thatmay be controlled by the controller of the apparatus (not shown in FIG.37) to regulate the flow of fluid in the cartridge. As shown in FIG. 38the linear actuator may be coupled to a ball coupler assembly 3708 thatmay provide a means of moving a base plate up and down (opening andclosing) which holds the cartridge in place during a scan. Thismechanism does not bind and is not subject to axial alignment issuesbecause the ball plunger and ball plunger coupler 3804 are not rigidlycoupled. Also, the contact surfaces between the two parts are a radiusand a plane, again removing any alignment issues. In this example, thecartridge holder includes a clamp base that rides on linear bearings.

FIGS. 40-42 show one example of the placement of the chip (e.g.,photonic chip) for use in their investigation. As shown in FIG. 41, thechip may be positioned in a chip pocket within the cartridge andconnected to the fluid channels for washing, binding, rinsing, etc.

Any of the methods (including user interfaces) described herein may beimplemented as software, hardware or firmware, and may be described as anon-transitory computer-readable storage medium storing a set ofinstructions capable of being executed by a processor (e.g., computer,tablet, smartphone, etc.), that when executed by the processor causesthe processor to control perform any of the steps, including but notlimited to: displaying, communicating with the user, analyzing,modifying parameters (including timing, frequency, intensity, etc.),determining, alerting, or the like.

When a feature or element is herein referred to as being “on” anotherfeature or element, it can be directly on the other feature or elementor intervening features and/or elements may also be present. Incontrast, when a feature or element is referred to as being “directlyon” another feature or element, there are no intervening features orelements present. It will also be understood that, when a feature orelement is referred to as being “connected”, “attached” or “coupled” toanother feature or element, it can be directly connected, attached orcoupled to the other feature or element or intervening features orelements may be present. In contrast, when a feature or element isreferred to as being “directly connected”, “directly attached” or“directly coupled” to another feature or element, there are nointervening features or elements present. Although described or shownwith respect to one embodiment, the features and elements so describedor shown can apply to other embodiments. It will also be appreciated bythose of skill in the art that references to a structure or feature thatis disposed “adjacent” another feature may have portions that overlap orunderlie the adjacent feature.

Terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention.For example, as used herein, the singular forms “a”, “an” and “the” areintended to include the plural forms as well, unless the context clearlyindicates otherwise. It will be further understood that the terms“comprises” and/or “comprising,” when used in this specification,specify the presence of stated features, steps, operations, elements,and/or components, but do not preclude the presence or addition of oneor more other features, steps, operations, elements, components, and/orgroups thereof. As used herein, the term “and/or” includes any and allcombinations of one or more of the associated listed items and may beabbreviated as “/”.

Spatially relative terms, such as “under”, “below”, “lower”, “over”,“upper” and the like, may be used herein for ease of description todescribe one element or feature's relationship to another element(s) orfeature(s) as illustrated in the figures. It will be understood that thespatially relative terms are intended to encompass differentorientations of the device in use or operation in addition to theorientation depicted in the figures. For example, if a device in thefigures is inverted, elements described as “under” or “beneath” otherelements or features would then be oriented “over” the other elements orfeatures. Thus, the exemplary term “under” can encompass both anorientation of over and under. The device may be otherwise oriented(rotated 90 degrees or at other orientations) and the spatially relativedescriptors used herein interpreted accordingly. Similarly, the terms“upwardly”, “downwardly”, “vertical”, “horizontal” and the like are usedherein for the purpose of explanation only unless specifically indicatedotherwise.

Although the terms “first” and “second” may be used herein to describevarious features/elements (including steps), these features/elementsshould not be limited by these terms, unless the context indicatesotherwise. These terms may be used to distinguish one feature/elementfrom another feature/element. Thus, a first feature/element discussedbelow could be termed a second feature/element, and similarly, a secondfeature/element discussed below could be termed a first feature/elementwithout departing from the teachings of the present invention.

Throughout this specification and the claims which follow, unless thecontext requires otherwise, the word “comprise”, and variations such as“comprises” and “comprising” means various components can be co-jointlyemployed in the methods and articles (e.g., compositions and apparatusesincluding device and methods). For example, the term “comprising” willbe understood to imply the inclusion of any stated elements or steps butnot the exclusion of any other elements or steps.

In general, any of the apparatuses and methods described herein shouldbe understood to be inclusive, but all or a sub-set of the componentsand/or steps may alternatively be exclusive, and may be expressed as“consisting of” or alternatively “consisting essentially of” the variouscomponents, steps, sub-components or sub-steps.

As used herein in the specification and claims, including as used in theexamples and unless otherwise expressly specified, all numbers may beread as if prefaced by the word “about” or “approximately,” even if theterm does not expressly appear. The phrase “about” or “approximately”may be used when describing magnitude and/or position to indicate thatthe value and/or position described is within a reasonable expectedrange of values and/or positions. For example, a numeric value may havea value that is +/−0.1% of the stated value (or range of values), +/−1%of the stated value (or range of values), +/−2% of the stated value (orrange of values), +/−5% of the stated value (or range of values), +/−10%of the stated value (or range of values), etc. Any numerical valuesgiven herein should also be understood to include about or approximatelythat value, unless the context indicates otherwise. For example, if thevalue “10” is disclosed, then “about 10” is also disclosed. Anynumerical range recited herein is intended to include all sub-rangessubsumed therein. It is also understood that when a value is disclosedthat “less than or equal to” the value, “greater than or equal to thevalue” and possible ranges between values are also disclosed, asappropriately understood by the skilled artisan. For example, if thevalue “X” is disclosed the “less than or equal to X” as well as “greaterthan or equal to X” (e.g., where X is a numerical value) is alsodisclosed. It is also understood that the throughout the application,data is provided in a number of different formats, and that this data,represents endpoints and starting points, and ranges for any combinationof the data points. For example, if a particular data point “10” and aparticular data point “15” are disclosed, it is understood that greaterthan, greater than or equal to, less than, less than or equal to, andequal to 10 and 15 are considered disclosed as well as between 10 and15. It is also understood that each unit between two particular unitsare also disclosed. For example, if 10 and 15 are disclosed, then 11,12, 13, and 14 are also disclosed.

Although various illustrative embodiments are described above, any of anumber of changes may be made to various embodiments without departingfrom the scope of the invention as described by the claims. For example,the order in which various described method steps are performed mayoften be changed in alternative embodiments, and in other alternativeembodiments one or more method steps may be skipped altogether. Optionalfeatures of various device and system embodiments may be included insome embodiments and not in others. Therefore, the foregoing descriptionis provided primarily for exemplary purposes and should not beinterpreted to limit the scope of the invention as it is set forth inthe claims.

The examples and illustrations included herein show, by way ofillustration and not of limitation, specific embodiments in which thesubject matter may be practiced. As mentioned, other embodiments may beutilized and derived there from, such that structural and logicalsubstitutions and changes may be made without departing from the scopeof this disclosure. Such embodiments of the inventive subject matter maybe referred to herein individually or collectively by the term“invention” merely for convenience and without intending to voluntarilylimit the scope of this application to any single invention or inventiveconcept, if more than one is, in fact, disclosed. Thus, althoughspecific embodiments have been illustrated and described herein, anyarrangement calculated to achieve the same purpose may be substitutedfor the specific embodiments shown. This disclosure is intended to coverany and all adaptations or variations of various embodiments.Combinations of the above embodiments, and other embodiments notspecifically described herein, will be apparent to those of skill in theart upon reviewing the above description.

What is claimed is:
 1. A method of reading optical signals from aphotonic chip of a removable cartridge head in an optical reader, themethod comprising: aligning a scan head of the optical reader with thechip so that the chip and a laser source, a plurality of fibers, and anoptical sensor of the scan head are aligned along a polarization axiswith the chip; maintaining a polarization of the polarization axis in atransverse-magnetic (TM) polarization; and emitting one or more beams oflight from the laser, through the plurality of fibers and into an edgeof the photonic chip in the TM polarization; and detecting, in theoptical sensor, TM polarized light from one or more waveguides withinthe chip when the one or more beams of light interact with an analytemolecule on the chip.
 2. The method of claim 1, further comprisinginserting a cartridge containing the chip into the optical reader. 3.The method of claim 1, wherein emitting comprises emitting a pluralityof concurrent beams of TM polarized light from the scan head, into theedge of the photonic chip.
 4. The method of claim 1, wherein maintainingthe polarization of the polarization axis comprises maintaining thepolarization of the plurality of fibers.
 5. The method of claim 1,further comprising polarizing light emitted from the scan to the edge ofthe chip in a polarizer.
 6. The method of claim 1, further comprisingadjusting the alignment of the scan head while emitting and/or detectingto maintain the TM polarization.
 7. An optical reader device for readinga photonic chip of a removable cartridge, the device comprising: a scanhead; a plurality of laser sources each configured to emit light havinga TM polarization; a first plurality of optical fibers, wherein eachlaser source is coupled to one optical fiber of the first plurality ofoptical fibers, further wherein the first plurality of optical fibersare polarization maintaining single-mode fibers; a plurality of opticalsensors; a second plurality of optical fibers, wherein each opticalsensor is coupled to one optical fiber of the second plurality ofoptical fibers, further wherein the second plurality of optical fibersare multimode fibers; wherein each of the first plurality of opticalfibers and the second plurality of optical fibers terminates on the scanhead so that an end of each optical fiber of the first and secondpluralities of optical fibers are arranged in a line facing a gap; and acartridge holder configured to receive the removable cartridge so thatthe photonic chip is aligned with a polarization axis formed by the scanhead so that an end of the photonic chip comprising a plurality ofwaveguides faces the gap, across from the scan head, wherein the deviceis configured to maintain the polarization of the polarization axis in atransverse-magnetic (TM) polarization.
 8. The device of claim 7, whereinthe laser sources comprise diode lasers.
 9. The device of claim 7,wherein the second plurality of fibers at least twice as many opticalfibers as the first plurality of fibers.
 10. The device of claim 7,further comprising a controller configured to control alignment of thescan head relative to the cartridge.
 11. The device of claim 7, furtherwherein the cartridge holder is configured to clamp the cartridge toprevent it from moving.
 12. The device of claim 7, wherein the cartridgeholder is configured to bias the cartridge in normal to a major plane ofthe cartridge against a reference surface to prevent movement of thecartridge as one or more actuators apply force to the cartridge to drivefluid through the cartridge.
 13. The device of claim 7, wherein thecontroller is configured to adjust the position of the scan head duringoperation of the device by actuating a scan head actuator to align theends of the optical fibers with waveguides of the photonic chip when thecartridge is in the cartridge holder.
 14. An optical reader device forreading a photonic chip of a removable cartridge, the device comprising:a cartridge holder comprising a slot extending into the reader, the slothaving a height and a width; a scan head, wherein the scan headcomprises a first plurality of optical fiber ends that are opticallyconnected to one or more laser light sources and a second plurality offiber ends that are optically connected to a plurality of detectors; ascan head actuator configured to move the scan head relative to thecartridge holder; a plurality of valves on the cartridge holder that areconfigured to couple with valve openings in the removable cartridge; apump membrane actuator on the cartridge holder that is configured toapply force to a membrane pump of the removable cartridge, wherein thepump membrane actuator is configured to hold a plurality of extendedpositions to deflect or relax deflection of the membrane pump; and acontroller configured to coordinate movement of the scan head,illumination of the one or more laser light sources, detection by theplurality of detectors, opening and closing of the plurality of valvesand positioning of the pump membrane actuator when the removablecartridge is inserted into the cartridge holder.
 15. The device of claim14, wherein the controller is configured to clamp the cartridge holderwhen the removable cartridge is inserted into the cartridge holder. 16.The device of claim 14, wherein the scan head comprises a linear arrayof the first plurality of optical fiber ends and the second plurality ofoptical fiber ends.
 17. The device of claim 14, wherein each valve ofthe plurality of valves comprises a seal configured to be moved relativeto the cartridge holder to open or close a valve opening in theremovable cartridge when the removable cartridge is held within thecartridge holder.
 18. The device of claim 14, wherein the pump membraneactuator comprises an arm and a driver.
 19. The device of claim 14,wherein the pump membrane actuator comprises a rounded, ball-shaped end.20. The device of claim 14, wherein the pump membrane actuator comprisesa rocker arm that is motor driven.